5V01 | pdb_00005v01

Crystal structure of the competence damage-inducible protein A (ComA) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578

• PDB DOI: https://doi.org/10.2210/pdb5V01/pdb

• Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-28 Released: 2017-03-15 
• Deposition Author(s): Borek, D., Wawrzak, Z., Grimshaw, S., Sandoval, J., Evdokimova, E., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the competence damage-inducible protein A (ComA) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578

Borek, D.

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: 36.67 kDa 
• Atom Count: 2,947 
• Modeled Residue Count: 330 
• Deposited Residue Count: 347 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Competence damage-inducible protein A	A, B	173	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: ydeJ, KPN_01597
UniProt
Find proteins for A6T8V7 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T8V7  Go to UniProtKB:  A6T8V7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35v01

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.452	α = 90
b = 90.433	β = 103.75
c = 44.126	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Borek, D., Wawrzak, Z., Grimshaw, S., Sandoval, J., Evdokimova, E., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272200700058C

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 2.0: 2023-02-22
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 2.2: 2023-11-15
  Changes: Data collection
• Version 2.3: 2024-11-20
  Changes: Structure summary