3OEE

Structure of four mutant forms of yeast F1 ATPase: alpha-F405S

PDB DOI: https://doi.org/10.2210/pdb3OEE/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2010-08-12 Released: 2010-09-15
Deposition Author(s): Arsenieva, D., Symersky, J., Wang, Y., Pagadala, V., Mueller, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.259
R-Value Work: 0.212
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of four mutant forms of yeast F1 ATPase: alpha-F405S

Arsenieva, D., Symersky, J., Wang, Y., Pagadala, V., Mueller, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 1,126.29 kDa
Atom Count: 72,675
Modelled Residue Count: 9,597
Deposited Residue Count: 10,377
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C, J, K A, B, C, J, K, L, S, T, U	510	Saccharomyces cerevisiae	Mutation(s): 1 Gene Names: ATP1, YBL099W, YBL0827 EC: 3.6.3.14
UniProt
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07251 Go to UniProtKB: P07251
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07251
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D, E, F, M, N D, E, F, M, N, O, V, W, X	484	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP2, YJR121W, J2041 EC: 3.6.3.14
UniProt
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00830 Go to UniProtKB: P00830
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00830
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit gamma	G, P, Y	278	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP3, ATP3a, ATP3b, YBR039W, YBR0408 EC: 3.6.3.14
UniProt
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38077 Go to UniProtKB: P38077
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38077
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit delta	H, Q, Z	138	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP16, YDL004W, YD8119.03, D2935 EC: 3.6.3.14
UniProt
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12165 Go to UniProtKB: Q12165
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12165
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit epsilon	AA [auth 1], I, R	61	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATP15, YPL271W, P0345 EC: 3.6.3.14
UniProt
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21306 Go to UniProtKB: P21306
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21306
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain BB [auth U] SDF format, chain DA [auth B] SDF format, chain DB [auth V] SDF format, chain FA [auth C] SDF format, chain FB [auth X] SDF format, chain HA [auth D] SDF format, chain KA [auth F] SDF format, chain MA [auth J] SDF format, chain OA [auth K] SDF format, chain QA [auth L] SDF format, chain SA [auth M] SDF format, chain VA [auth O] SDF format, chain XA [auth S] SDF format, chain ZA [auth T] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth U] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth V] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth X] MOL2 format, chain HA [auth D] MOL2 format, chain KA [auth F] MOL2 format, chain MA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain QA [auth L] MOL2 format, chain SA [auth M] MOL2 format, chain VA [auth O] MOL2 format, chain XA [auth S] MOL2 format, chain ZA [auth T]	BA [auth A] BB [auth U] DA [auth B] DB [auth V] FA [auth C] BA [auth A], BB [auth U], DA [auth B], DB [auth V], FA [auth C], FB [auth X], HA [auth D], KA [auth F], MA [auth J], OA [auth K], QA [auth L], SA [auth M], VA [auth O], XA [auth S], ZA [auth T]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain BA [auth A] Focus chain BB [auth U] Focus chain DA [auth B] Focus chain DB [auth V] Focus chain FA [auth C] Focus chain FB [auth X] Focus chain HA [auth D] Focus chain KA [auth F] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain QA [auth L] Focus chain SA [auth M] Focus chain VA [auth O] Focus chain XA [auth S] Focus chain ZA [auth T] Interactions & Density Focus chain BA [auth A] Focus chain BB [auth U] Focus chain DA [auth B] Focus chain DB [auth V] Focus chain FA [auth C] Focus chain FB [auth X] Focus chain HA [auth D] Focus chain KA [auth F] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain QA [auth L] Focus chain SA [auth M] Focus chain VA [auth O] Focus chain XA [auth S] Focus chain ZA [auth T]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain UA [auth N] MOL2 format, chain JA [auth E] MOL2 format, chain UA [auth N]	JA [auth E], UA [auth N]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain JA [auth E] Focus chain UA [auth N] Interactions & Density Focus chain JA [auth E] Focus chain UA [auth N]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth T] SDF format, chain CA [auth A] SDF format, chain CB [auth U] SDF format, chain EA [auth B] SDF format, chain EB [auth V] SDF format, chain GA [auth C] SDF format, chain GB [auth X] SDF format, chain IA [auth D] SDF format, chain LA [auth F] SDF format, chain NA [auth J] SDF format, chain PA [auth K] SDF format, chain RA [auth L] SDF format, chain TA [auth M] SDF format, chain WA [auth O] SDF format, chain YA [auth S] MOL2 format, chain AB [auth T] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth U] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth V] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth X] MOL2 format, chain IA [auth D] MOL2 format, chain LA [auth F] MOL2 format, chain NA [auth J] MOL2 format, chain PA [auth K] MOL2 format, chain RA [auth L] MOL2 format, chain TA [auth M] MOL2 format, chain WA [auth O] MOL2 format, chain YA [auth S]	AB [auth T] CA [auth A] CB [auth U] EA [auth B] EB [auth V] AB [auth T], CA [auth A], CB [auth U], EA [auth B], EB [auth V], GA [auth C], GB [auth X], IA [auth D], LA [auth F], NA [auth J], PA [auth K], RA [auth L], TA [auth M], WA [auth O], YA [auth S]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth T] Focus chain CA [auth A] Focus chain CB [auth U] Focus chain EA [auth B] Focus chain EB [auth V] Focus chain GA [auth C] Focus chain GB [auth X] Focus chain IA [auth D] Focus chain LA [auth F] Focus chain NA [auth J] Focus chain PA [auth K] Focus chain RA [auth L] Focus chain TA [auth M] Focus chain WA [auth O] Focus chain YA [auth S] Interactions & Density Focus chain AB [auth T] Focus chain CA [auth A] Focus chain CB [auth U] Focus chain EA [auth B] Focus chain EB [auth V] Focus chain GA [auth C] Focus chain GB [auth X] Focus chain IA [auth D] Focus chain LA [auth F] Focus chain NA [auth J] Focus chain PA [auth K] Focus chain RA [auth L] Focus chain TA [auth M] Focus chain WA [auth O] Focus chain YA [auth S]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.259
R-Value Work: 0.212
R-Value Observed: 0.213
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.43	α = 90
b = 288.58	β = 101.37
c = 187.17	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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3OEE

Structure of four mutant forms of yeast F1 ATPase: alpha-F405S

Structure of four mutant forms of yeast F1 ATPase: alpha-F405S

Entity ID: 1

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Experimental Data

Structure Validation

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Deposition Data

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