3BY5

Crystal structure of cobalamin biosynthesis protein chiG from Agrobacterium tumefaciens str. C58

• PDB DOI: https://doi.org/10.2210/pdb3BY5/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-15 Released: 2008-01-22 
• Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Sojitra, S., Rutter, M., Iizuka, M., Maletic, M., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal structure of cobalamin biosynthesis protein from Agrobacterium tumefaciens str. C58.

Patskovsky, Y., Bonanno, J.B., Sojitra, S., Rutter, M., Iizuka, M., Maletic, M., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.98 kDa 
• Atom Count: 864 
• Modelled Residue Count: 123 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalamin biosynthesis protein	A	155	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: chiG
UniProt
Find proteins for A9CHC6 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CHC6  Go to UniProtKB:  A9CHC6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.52 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.023	α = 90
b = 72.023	β = 90
c = 141.069	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-22 
Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Sojitra, S., Rutter, M., Iizuka, M., Maletic, M., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Structure summary