2HMC | pdb_00002hmc

The Crystal Structure of Dihydrodipicolinate Synthase DapA from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb2HMC/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-07-11 Released: 2006-09-05 
• Deposition Author(s): Kim, Y., Zhang, R., Xu, X., Zheng, H., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

The Crystal Structure of Dihydrodipicolinate Synthase DapA from Agrobacterium tumefaciens

Kim, Y., Zhang, R., Xu, X., Zheng, H., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 37.69 kDa 
• Atom Count: 2,924 
• Modeled Residue Count: 314 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A	344	Agrobacterium fabrum str. C58	Mutation(s): 10  Gene Names: dapA
UniProt
Find proteins for A9CGZ4 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CGZ4  Go to UniProtKB:  A9CGZ4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.102	α = 90
b = 101.102	β = 90
c = 120.914	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-05 
Deposition Author(s): Kim, Y., Zhang, R., Xu, X., Zheng, H., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-09-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary