3LMM | pdb_00003lmm

Crystal Structure of the DIP2311 protein from Corynebacterium diphtheriae, Northeast Structural Genomics Consortium Target CdR35

• PDB DOI: https://doi.org/10.2210/pdb3LMM/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-31 Released: 2010-02-16 
• Deposition Author(s): Forouhar, F., Lew, S., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Buchwald, W.A., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, 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: 3.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Northeast Structural Genomics Consortium Target CdR35

Forouhar, F., Lew, S., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Buchwald, W.A., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 258.08 kDa 
• Atom Count: 16,408 
• Modeled Residue Count: 2,080 
• Deposited Residue Count: 2,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	583	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: DIP2311
UniProt
Find proteins for Q6NEG3 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEG3  Go to UniProtKB:  Q6NEG3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	E [auth A], I [auth B], K [auth C], M [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth A], J [auth B], L [auth C], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.306	α = 90
b = 102.03	β = 116
c = 164.515	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SHELX	data scaling
SOLVE	phasing
RESOLVE	phasing
SHELX	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Forouhar, F., Lew, S., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Buchwald, W.A., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary