3LYU | pdb_00003lyu

Crystal Structure of the C-terminal domain (residues 83-215) of PF1911 hydrogenase from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR246A

PDB DOI: https://doi.org/10.2210/pdb3LYU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-02-28 Released: 2010-03-23
Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Sahdev, S., Xiao, R., Foote, E.L., Ciccosanti, C., Belote, R.L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Northeast Structural Genomics Consortium Target PfR246A

Forouhar, F., Abashidze, M., Seetharaman, J., Sahdev, S., Xiao, R., Foote, E.L., Ciccosanti, C., Belote, R.L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 98.48 kDa
Atom Count: 6,280
Modeled Residue Count: 783
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hydrogenase	A, B, C, D, E A, B, C, D, E, F	142	Pyrococcus furiosus	Mutation(s): 0 Gene Names: PF1911
UniProt
Find proteins for Q8TZS3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZS3 Go to UniProtKB: Q8TZS3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TZS3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	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: 0.237 (Depositor), 0.237 (DCC)
R-Value Work: 0.210 (Depositor), 0.212 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.654	α = 90
b = 77.654	β = 90
c = 117.513	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-23

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Data collection, Database references, Structure summary