2WU5

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD His71Met mutant

PDB DOI: https://doi.org/10.2210/pdb2WU5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2009-09-29 Released: 2010-08-25
Deposition Author(s): Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.252
R-Value Work: 0.213
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd His71met Mutant

Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

To be published.

Macromolecule Content

Total Structure Weight: 363.3 kDa
Atom Count: 25,164
Modelled Residue Count: 3,159
Deposited Residue Count: 3,210
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT	A, E, I	588	Escherichia coli	Mutation(s): 0 EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12)) Explore P0AC41 Go to UniProtKB: P0AC41
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AC41
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT	B, F, J	238	Escherichia coli	Mutation(s): 0 EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P07014 (Escherichia coli (strain K12)) Explore P07014 Go to UniProtKB: P07014
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07014
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT	C, G, K	129	Escherichia coli	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P69054 (Escherichia coli (strain K12)) Explore P69054 Go to UniProtKB: P69054
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69054
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT	D, H, L	115	Escherichia coli	Mutation(s): 1 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P0AC44 (Escherichia coli (strain K12)) Explore P0AC44 Go to UniProtKB: P0AC44
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AC44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain M [auth A] SDF format, chain U [auth E] MOL2 format, chain CA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain U [auth E]	CA [auth I], M [auth A], U [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain CA [auth I] Focus chain M [auth A] Focus chain U [auth E] Interactions & Density Focus chain CA [auth I] Focus chain M [auth A] Focus chain U [auth E]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain IA [auth K] SDF format, chain S [auth C] MOL2 format, chain AA [auth G] MOL2 format, chain IA [auth K] MOL2 format, chain S [auth C]	AA [auth G], IA [auth K], S [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth G] Focus chain IA [auth K] Focus chain S [auth C] Interactions & Density Focus chain AA [auth G] Focus chain IA [auth K] Focus chain S [auth C]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain Y [auth F] SDF format, chain GA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth F] MOL2 format, chain GA [auth J]	GA [auth J], Q [auth B], Y [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain GA [auth J] Focus chain Q [auth B] Focus chain Y [auth F] Interactions & Density Focus chain GA [auth J] Focus chain Q [auth B] Focus chain Y [auth F]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain HA [auth J] SDF format, chain R [auth B] SDF format, chain Z [auth F] MOL2 format, chain HA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth F]	HA [auth J], R [auth B], Z [auth F]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain HA [auth J] Focus chain R [auth B] Focus chain Z [auth F] Interactions & Density Focus chain HA [auth J] Focus chain R [auth B] Focus chain Z [auth F]
CBE Query on CBE Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain JA [auth K] SDF format, chain T [auth C] MOL2 format, chain BA [auth G] MOL2 format, chain JA [auth K] MOL2 format, chain T [auth C]	BA [auth G], JA [auth K], T [auth C]	2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE C₁₂ H₁₃ N O₂ S GYSSRZJIHXQEHQ-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain JA [auth K] Focus chain T [auth C] Interactions & Density Focus chain BA [auth G] Focus chain JA [auth K] Focus chain T [auth C]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain FA [auth J] SDF format, chain X [auth F] MOL2 format, chain P [auth B] MOL2 format, chain FA [auth J] MOL2 format, chain X [auth F]	FA [auth J], P [auth B], X [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain FA [auth J] Focus chain P [auth B] Focus chain X [auth F] Interactions & Density Focus chain FA [auth J] Focus chain P [auth B] Focus chain X [auth F]
TEO Query on TEO Download Ideal Coordinates CCD File SDF format, chain DA [auth I] SDF format, chain N [auth A] SDF format, chain V [auth E] MOL2 format, chain DA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain V [auth E]	DA [auth I], N [auth A], V [auth E]	MALATE LIKE INTERMEDIATE C₄ H₄ O₅ QFBHYOKSQPPXHZ-UWTATZPHSA-L		Interactions Focus chain DA [auth I] Focus chain N [auth A] Focus chain V [auth E] Interactions & Density Focus chain DA [auth I] Focus chain N [auth A] Focus chain V [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth I] SDF format, chain O [auth A] SDF format, chain W [auth E] MOL2 format, chain EA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain W [auth E]	EA [auth I], O [auth A], W [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth I] Focus chain O [auth A] Focus chain W [auth E] Interactions & Density Focus chain EA [auth I] Focus chain O [auth A] Focus chain W [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.252
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.06	α = 90
b = 183.82	β = 90
c = 203.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-11-20
Changes: Advisory, Derived calculations, Other
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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2WU5

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD His71Met mutant

Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd His71met Mutant

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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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

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