Download MendeleyCrystal structure of Dihydrodipicolinate synthase (TM1521) from Thermotoga maritima at 1.80 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
1O5K | pdb_00001o5k
Crystal structure of Dihydrodipicolinate synthase (TM1521) from Thermotoga maritima at 1.80 A resolution
- PDB DOI: https://doi.org/10.2210/pdb1O5K/pdb
- Classification: LYASE
- Organism(s): Thermotoga maritima MSB8
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2003-09-22 Released: 2003-10-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.186 (Depositor), 0.190 (DCC)
- R-Value Work: 0.139 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.142 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 2.3 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 |
| 4-hydroxy-tetrahydrodipicolinate synthase | 306 | Thermotoga maritima MSB8 | Mutation(s): 0 Gene Names: dapA, TM_1521 EC: 4.3.3.7 |  | |
UniProt | |||||
Find proteins for Q9X1K9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1K9 Go to UniProtKB: Q9X1K9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9X1K9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| KPI Query on KPI | A, B | L-PEPTIDE LINKING | C9 H16 N2 O4 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.186 (Depositor), 0.190 (DCC)
- R-Value Work: 0.139 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.142 (Depositor)
Diffraction Data: https://doi.org/10.18430/M31O5K
Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 54.672 | α = 90 |
| b = 140.768 | β = 90 |
| c = 155.943 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
Entry History
Deposition Data
- Released Date: 2003-10-07 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2003-10-07
Type: Initial release - Version 1.1: 2007-12-20
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance - Version 1.3: 2017-10-04
Changes: Refinement description - Version 1.4: 2017-10-25
Changes: Author supporting evidence - Version 2.0: 2018-05-30
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary - Version 2.1: 2018-07-18
Changes: Data collection, Database references - Version 2.2: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 2.3: 2023-11-29
Changes: Data collection
