Download MendeleyCrystal structure of cobalamin synthesis related protein (CobF) from Corynebacterium diphtheriae
Nocek, B., Zhou, M., Clancy, S., Joachimiak, A.To be published.
2NPN
Crystal structure of putative cobalamin synthesis related protein (CobF) from Corynebacterium diphtheriae
- PDB DOI: https://doi.org/10.2210/pdb2NPN/pdb
- Classification: TRANSFERASE
- Organism(s): Corynebacterium diphtheriae
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2006-10-27 Released: 2006-11-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.198
- R-Value Work: 0.172
- R-Value Observed: 0.173
This is version 1.2 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 |
| Putative cobalamin synthesis related protein | A | 251 | Corynebacterium diphtheriae | Mutation(s): 5 |  |
UniProt | |||||
Find proteins for Q6NIF5 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NIF5 Go to UniProtKB: Q6NIF5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6NIF5 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SAM Query on SAM | C [auth A] | S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N |  | Ligand Interaction | |
| GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| MG Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
| 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: 1.60 Å
- R-Value Free: 0.198
- R-Value Work: 0.172
- R-Value Observed: 0.173
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 77.104 | α = 90 |
| b = 80.845 | β = 90 |
| c = 76.976 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| SHELXD | phasing |
| SHELXE | model building |
| MLPHARE | phasing |
| DM | phasing |
| SOLVE | phasing |
| RESOLVE | phasing |
| ARP/wARP | model building |
| CCP4 | phasing |
| O | model building |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2006-11-28 Deposition Author(s): Nocek, B., Zhou, M., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2006-11-28
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
