1YD7

Conserved hypothetical protein Pfu-1647980-001 from Pyrococcus furiosus

PDB DOI: https://doi.org/10.2210/pdb1YD7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-12-23 Released: 2005-02-08
Deposition Author(s): Horanyi, P., Florence, Q., Zhou, W., Chang, J., Zhao, M., Habel, J., Xu, H., Chen, L., Lee, D., Nguyen, D., Chang, S.-H., Tempel, W., Lin, D., Zhang, H., Praissman, J., Jenney Jr., F.E., Adams, M.W.W., Liu, Z.-J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.243
R-Value Work: 0.206
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

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

Literature

Conserved hypothetical protein Pfu-1647980-001 from Pyrococcus furiosus

Horanyi, P., Florence, Q., Zhou, W., Chang, J., Zhao, M., Habel, J., Xu, H., Chen, L., Lee, D., Nguyen, D., Chang, S.-H., Tempel, W., Lin, D., Zhang, H., Praissman, J., Jenney Jr., F.E., Adams, M.W.W., Liu, Z.-J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

To be published.

Macromolecule Content

Total Structure Weight: 44.66 kDa
Atom Count: 1,310
Modelled Residue Count: 169
Deposited Residue Count: 395
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-keto acid:ferredoxin oxidoreductase subunit alpha	A	395	Pyrococcus furiosus	Mutation(s): 12
UniProt
Find proteins for Q8U046 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U046 Go to UniProtKB: Q8U046
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U046
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.243
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.448	α = 90
b = 61.448	β = 90
c = 129.084	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-02-08

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

Revision History (Full details and data files)

Version 1.0: 2005-02-08
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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1YD7

Conserved hypothetical protein Pfu-1647980-001 from Pyrococcus furiosus

Conserved hypothetical protein Pfu-1647980-001 from Pyrococcus furiosus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)