Download MendeleyRe-Establishing a Metal-Binding Scaffold with Full Activity in the Metal-Independent Kdo8P Synthase from Neisseria Meningitidis
Cochrane, F.C., Patchett, M.L., Jameson, G.B., Parker, E.J.To be published.
2QKF
Crystal structure of 3-deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis
- PDB DOI: https://doi.org/10.2210/pdb2QKF/pdb
- Classification: TRANSFERASE
- Organism(s): Neisseria meningitidis serogroup B
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2007-07-11 Released: 2008-07-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.235
- R-Value Work: 0.196
- R-Value Observed: 0.197
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
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 |
| 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase | 280 | Neisseria meningitidis serogroup B | Mutation(s): 0 Gene Names: kdsA EC: 2.5.1.55 |  | |
UniProt | |||||
Find proteins for Q9JZ55 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JZ55 Go to UniProtKB: Q9JZ55 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9JZ55 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | I [auth C], J [auth C], K [auth C], N [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth B], F [auth C], G [auth C], L [auth D], M [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | H [auth C] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.235
- R-Value Work: 0.196
- R-Value Observed: 0.197
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 81.515 | α = 90 |
| b = 85.295 | β = 90 |
| c = 162.686 | γ = 90 |
| Software Name | Purpose |
|---|---|
| d*TREK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| d*TREK | data reduction |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2008-07-01 Deposition Author(s): Cochrane, F.C., Patchett, M.L., Jameson, G.B., Parker, E.J.
Revision History (Full details and data files)
- Version 1.0: 2008-07-01
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
