Download MendeleyRedox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough
Marques, M.C., Coelho, R., Pereira, I.A.C., Matias, P.M.(2013) Int J Hydrogen Energy 38: 8664
3ZE9
3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the oxidized as-isolated state at 1.33 Angstroms
- PDB DOI: 10.2210/pdb3ZE9/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Desulfovibrio vulgaris str. Hildenborough
- Mutation(s): Yes
- Deposited: 2012-12-03 Released: 2013-06-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 Å
- R-Value Free: 0.148
- R-Value Work: 0.131
- R-Value Observed: 0.132
wwPDB Validation 3D Report Full Report
This is version 2.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT | A | 283 | Desulfovibrio vulgaris str. Hildenborough | Mutation(s): 0 Gene Names: hysB, DVU_1917 EC: 1.12.7.2 (PDB Primary Data), 1.12.2.1 (UniProt) |  |
UniProt | |||||
Find proteins for Q72AS4 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS4 Go to UniProtKB: Q72AS4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q72AS4 | ||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING | B | 484 | Desulfovibrio vulgaris str. Hildenborough | Mutation(s): 1 Gene Names: hysA, DVU_1918 EC: 1.12.7.2 |  |
UniProt | |||||
Find proteins for Q72AS3 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS3 Go to UniProtKB: Q72AS3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q72AS3 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FSX Query on FSX | E [auth A] | BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) Fe4 O3 S3 BIOGFUMNBIDAOG-VNBKSMEUCR |  | Ligand Interaction | |
| SF4 Query on SF4 | C [auth A], D [auth A] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC |  | Ligand Interaction | |
| FCO Query on FCO | F [auth B] | CARBONMONOXIDE-(DICYANO) IRON C3 Fe N2 O VBQUCMTXYFMTTE-UHFFFAOYSA-N |  | Ligand Interaction | |
| NI Query on NI | G [auth B] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | Ligand Interaction | |
| FE2 Query on FE2 | H [auth B] | FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | I [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| Modified Residues 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSS Query on CSS | A | L-PEPTIDE LINKING | C3 H7 N O2 S2 |  | CYS |
| OCS Query on OCS | B | L-PEPTIDE LINKING | C3 H7 N O5 S |  | CYS |
| PSW Query on PSW | B | L-PEPTIDE LINKING | C3 H7 N O2 S Se |  | SEC |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 Å
- R-Value Free: 0.148
- R-Value Work: 0.131
- R-Value Observed: 0.132
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 106.694 | α = 90 |
| b = 63.348 | β = 105.42 |
| c = 109.74 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Deposited Date: 2012-12-03
- Released Date: 2013-06-12 Deposition Author(s): Marques, M.C., Coelho, R., Pereira, I.A.C., Matias, P.M.
Revision History (Full details and data files)
- Version 1.0: 2013-06-12
Type: Initial release - Version 1.1: 2014-02-19
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description - Version 1.2: 2014-05-14
Changes: Atomic model - Version 1.3: 2014-11-05
Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary - Version 1.4: 2018-06-27
Changes: Advisory, Data collection, Derived calculations - Version 2.0: 2019-04-24
Changes: Atomic model, Data collection, Experimental preparation, Polymer sequence
