4JB7 | pdb_00004jb7

1.42 Angstrom resolution crystal structure of accessory colonization factor AcfC (acfC) in complex with D-aspartic acid

• PDB DOI: https://doi.org/10.2210/pdb4JB7/pdb

• Classification: CELL INVASION
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-19 Released: 2013-04-17 
• Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Dubrovska, I., Winsor, J., Minasov, G., Shuvalova, L., Filippova, E.V., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.141 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.125 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Literature

1.42 Angstrom resolution crystal structure of accessory colonization factor AcfC (acfC) in complex with D-aspartic acid

Halavaty, A.S., Wawrzak, Z., Dubrovska, I., Winsor, J., Minasov, G., Shuvalova, L., Filippova, E.V., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 29.38 kDa 
• Atom Count: 2,355 
• Modeled Residue Count: 233 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Accessory colonization factor AcfC	A	256	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: acfC, VC_0841
UniProt
Find proteins for Q9KTQ6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTQ6  Go to UniProtKB:  Q9KTQ6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	D [auth A], E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MLT	B [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.141 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.125 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34jb7

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.343	α = 90
b = 72.343	β = 90
c = 87.883	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Dubrovska, I., Winsor, J., Minasov, G., Shuvalova, L., Filippova, E.V., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary