3CBW | pdb_00003cbw

Crystal structure of the YdhT protein from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb3CBW/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-02-23 Released: 2008-03-11 
• Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Iizuka, M., Romero, R., Smith, D., Wasserman, S., 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: 1.27 Å
• R-Value Free: 
  0.172 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Crystal structure of the YdhT protein from Bacillus subtilis.

Bonanno, J.B., Rutter, M., Bain, K.T., Iizuka, M., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 80.65 kDa 
• Atom Count: 6,012 
• Modeled Residue Count: 666 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YdhT protein	A, B	353	Bacillus subtilis	Mutation(s): 3  Gene Names: ydhT, BSU05880 EC: 3.2.1.78
UniProt
Find proteins for O05512 (Bacillus subtilis (strain 168)) Explore O05512  Go to UniProtKB:  O05512

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth B], D [auth B], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.172 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.728	α = 90
b = 69.619	β = 91.09
c = 72.505	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Iizuka, M., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: 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: 2021-10-20
  Changes: Database references
• Version 1.6: 2024-10-30
  Changes: Data collection, Structure summary