3LSO

Crystal structure of Putative membrane anchored protein from Corynebacterium diphtheriae

• PDB DOI: https://doi.org/10.2210/pdb3LSO/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-12 Released: 2010-02-23 
• Deposition Author(s): Chang, C., Sather, A., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.251 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 

Literature

Crystal structure of Putative membrane anchored protein from Corynebacterium diphtheriae

Chang, C., Sather, A., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 104.61 kDa 
• Atom Count: 6,657 
• Modelled Residue Count: 890 
• Deposited Residue Count: 978 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative membrane anchored protein	A	489	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: DIP2116
UniProt
Find proteins for Q6NEZ3 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEZ3  Go to UniProtKB:  Q6NEZ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative membrane anchored protein	B	489	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: DIP2116
UniProt
Find proteins for Q6NEZ3 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEZ3  Go to UniProtKB:  Q6NEZ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ	A	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.251 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.205	α = 90
b = 95.517	β = 90
c = 160.778	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Chang, C., Sather, A., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description