Download MendeleyKrypton Derivatization of [FeFe] Hydrogenase from Desulfovibrio desulfuricans Reveals its Gas Channel
Bikbaev, K., Harand, T., Scheuenstuhl, L., Carpentier, P., Martini, M.A., Birrell, J.A., Span, I.To be published.
8RTI
Desulfovibrio desulfuricans [FeFe] hydrogenase in the apo form derivatized with krypton
- PDB DOI: https://doi.org/10.2210/pdb8RTI/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Desulfovibrio desulfuricans
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-01-26 Released: 2025-02-12
- Funding Organization(s): German Research Foundation (DFG)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 ?
- R-Value Free: 0.194 (Depositor), 0.193 (DCC)
- R-Value Work: 0.170 (Depositor), 0.167 (DCC)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Periplasmic [Fe] hydrogenase large subunit | 405 | Desulfovibrio desulfuricans | Mutation(s): 0 Gene Names: hydA, DVU_1769 EC: 1.12.7.2 |  | |
UniProt | |||||
Find proteins for P07598 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07598 Go to UniProtKB: P07598 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07598 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Periplasmic [Fe] hydrogenase small subunit | 88 | Desulfovibrio desulfuricans | Mutation(s): 0 Gene Names: hydB, DVU_1770 EC: 1.12.7.2 |  | |
UniProt | |||||
Find proteins for P07603 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07603 Go to UniProtKB: P07603 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07603 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SF4 (Subject of Investigation/LOI) Query on SF4 | E [auth A], F [auth A], G [auth A] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N |  | ||
| PGE Query on PGE | H [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| KR (Subject of Investigation/LOI) Query on KR | C [auth A], D [auth A] | KRYPTON Kr DNNSSWSSYDEUBZ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 ?
- R-Value Free: 0.194 (Depositor), 0.193 (DCC)
- R-Value Work: 0.170 (Depositor), 0.167 (DCC)
Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 49.677 | ¦Á = 90 |
| b = 88.048 | ¦Â = 90 |
| c = 89.784 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| REFMAC | refinement |
| PHASER | phasing |
| Coot | model building |
| XDS | data reduction |
| Aimless | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-02-12 Deposition Author(s): Bikbaev, K., Carpentier, P., Harand, T., Scheuenstuhl, L., Span, I.
| Funding Organization | Location | Grant Number |
|---|---|---|
| German Research Foundation (DFG) | Germany | SP 1476/4-1 |
Revision History (Full details and data files)
- Version 1.0: 2025-02-12
Type: Initial release
