Macromolecule Content

Total Structure Weight: 105.10 kDa
Atom Count: 7538
Modelled Residue Count: 865
Deposited Residue Count: 912
Unique protein chains: 1

1VM6

Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution

DOI: 10.2210/pdb1VM6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-09-03 Released: 2004-09-21
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.213
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate reductase	A, B, C, D	228	Thermotoga maritima	Mutation(s): 0 Gene Names: dapB, TM1520 EC: 1.3.1.26 (PDB Primary Data), 1.17.1.8 (UniProt)
Find proteins for Q9X1K8 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)) Explore Q9X1K8 Go to UniProtKB: Q9X1K8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain G [A] SDF format, chain N [B] SDF format, chain T [C] SDF format, chain Y [D] MOL2 format, chain G [A] MOL2 format, chain N [B] MOL2 format, chain T [C] MOL2 format, chain Y [D]	A, B, C, D	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Ligand Interaction
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain O [B] SDF format, chain P [B] SDF format, chain Q [B] SDF format, chain V [C] MOL2 format, chain O [B] MOL2 format, chain P [B] MOL2 format, chain Q [B] MOL2 format, chain V [C]	B, C	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain U [C] MOL2 format, chain U [C]	C	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain F [A] SDF format, chain H [B] SDF format, chain I [B] SDF format, chain J [B] SDF format, chain K [B] SDF format, chain L [B] SDF format, chain M [B] SDF format, chain R [C] SDF format, chain S [C] SDF format, chain W [D] SDF format, chain X [D] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain H [B] MOL2 format, chain I [B] MOL2 format, chain J [B] MOL2 format, chain K [B] MOL2 format, chain L [B] MOL2 format, chain M [B] MOL2 format, chain R [C] MOL2 format, chain S [C] MOL2 format, chain W [D] MOL2 format, chain X [D]	A, B, C, D	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.213
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: C 1 2 1
Diffraction Data DOI: 10.18430/M31VM6 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.077	α = 90
b = 109.217	β = 119.23
c = 112.602	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2004-09-03
Released Date: 2004-09-21

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-09-21
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.