3KMI | pdb_00003kmi

Crystal structure of putative membrane protein from Clostridium difficile 630

• PDB DOI: https://doi.org/10.2210/pdb3KMI/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-11-10 Released: 2009-11-17 
• Deposition Author(s): Chang, C., Rakowski, E., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.235 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of putative membrane protein from Clostridium difficile 630

Chang, C., Rakowski, E., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 41.59 kDa 
• Atom Count: 3,362 
• Modeled Residue Count: 340 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative membrane protein COG4129	A, B	177	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD3042
UniProt
Find proteins for Q184N1 (Clostridioides difficile (strain 630)) Explore Q184N1  Go to UniProtKB:  Q184N1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	D [auth B], E [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.235 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.378	α = 90
b = 66.242	β = 90
c = 87.189	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: 2009-11-17 
Deposition Author(s): Chang, C., Rakowski, E., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary