3B4U | pdb_00003b4u

Crystal structure of dihydrodipicolinate synthase from Agrobacterium tumefaciens str. C58

PDB DOI: https://doi.org/10.2210/pdb3B4U/pdb

Classification: LYASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-10-24 Released: 2007-12-04
Deposition Author(s): Zhang, R., Xu, L., Gu, J., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.156 (Depositor), 0.152 (DCC)
R-Value Work:
0.127 (Depositor), 0.125 (DCC)
R-Value Observed:
0.128 (Depositor)

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This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of the dihydrodipicolinate synthase from Agrobacterium tumefaciens.

Zhang, R., Xu, L., Gu, J., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 62.6 kDa
Atom Count: 5,693
Modeled Residue Count: 575
Deposited Residue Count: 588
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	294	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: dapA, AGR_C_4548, Atu2503
UniProt
Find proteins for A9CHR2 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CHR2 Go to UniProtKB: A9CHR2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9CHR2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.156 (Depositor), 0.152 (DCC)
R-Value Work: 0.127 (Depositor), 0.125 (DCC)
R-Value Observed: 0.128 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.116	α = 79.35
b = 49.442	β = 89.06
c = 69.084	γ = 83.94

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-12-04

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-12-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.