3MCU | pdb_00003mcu

Crystal structure of the dipicolinate synthase chain B from Bacillus cereus. Northeast Structural Genomics Consortium Target BcR215.

• PDB DOI: https://doi.org/10.2210/pdb3MCU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-29 Released: 2010-04-14 
• Deposition Author(s): Vorobiev, S., Lew, S., Abashidze, M., Seetharaman, J., Wang, H., Ciccosanti, C., Foote, E.L., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.241 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the dipicolinate synthase chain B from Bacillus cereus.

Vorobiev, S., Lew, S., Abashidze, M., Seetharaman, J., Wang, H., Ciccosanti, C., Foote, E.L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

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 (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 140.56 kDa 
• Atom Count: 8,949 
• Modeled Residue Count: 1,116 
• Deposited Residue Count: 1,242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipicolinate synthase, B chain	A, B, C, D, E, F	207	Bacillus cereus ATCC 14579	Mutation(s): 0  Gene Names: BC_3800 EC: 1.3.1
UniProt
Find proteins for Q819Z6 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q819Z6  Go to UniProtKB:  Q819Z6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth C], I [auth C], J [auth D], K [auth E], L [auth E], M [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.241 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.082	α = 90
b = 129.257	β = 90
c = 132.184	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Vorobiev, S., Lew, S., Abashidze, M., Seetharaman, J., Wang, H., Ciccosanti, C., Foote, E.L., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection
• Version 1.6: 2024-11-27
  Changes: Structure summary