Download MendeleyCrystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
Kim, Y., Zhou, M., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)To be published.
3LER | pdb_00003ler
Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
- PDB DOI: https://doi.org/10.2210/pdb3LER/pdb
- Classification: LYASE
- Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-01-15 Released: 2010-01-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 ?
- R-Value Free: 0.190 (Depositor), 0.188 (DCC)
- R-Value Work: 0.152 (Depositor), 0.151 (DCC)
- R-Value Observed: 0.154 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 2.1 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 |
| Dihydrodipicolinate synthase | 301 | Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 | Mutation(s): 0 Gene Names: dapA EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt) |  | |
UniProt | |||||
Find proteins for Q9PPB4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PPB4 Go to UniProtKB: Q9PPB4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9PPB4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PEG Query on PEG | H [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A], I [auth C] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACY Query on ACY | J [auth D] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
| FMT Query on FMT | G [auth B] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
| MG Query on MG | F [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| KPI Query on KPI | A, B, C, D | L-PEPTIDE LINKING | C9 H16 N2 O4 |  | LYS |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 ?
- R-Value Free: 0.190 (Depositor), 0.188 (DCC)
- R-Value Work: 0.152 (Depositor), 0.151 (DCC)
- R-Value Observed: 0.154 (Depositor)
Diffraction Data: https://doi.org/10.18430/m33ler
Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 72.185 | α = 90 |
| b = 85.304 | β = 90 |
| c = 199.157 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| HKL-3000 | data collection |
| HKL-3000 | phasing |
| SHELXS | phasing |
| MLPHARE | phasing |
| RESOLVE | model building |
| SOLVE | phasing |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| RESOLVE | phasing |
Entry History
Deposition Data
- Released Date: 2010-01-26 Deposition Author(s): Kim, Y., Zhou, M., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2010-01-26
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 2.0: 2018-05-30
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary - Version 2.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary
