3PDW | pdb_00003pdw

Crystal structure of putative p-nitrophenyl phosphatase from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb3PDW/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-25 Released: 2010-11-17 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, 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: 1.60 Å
• R-Value Free: 
  0.211 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of putative p-nitrophenyl phosphatase from Bacillus subtilis

Fedorov, A.A., Fedorov, E.V., Toro, R., 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)

Macromolecule Content 

• Total Structure Weight: 29.44 kDa 
• Atom Count: 2,185 
• Modeled Residue Count: 257 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized hydrolase yutF	A	266	Bacillus subtilis	Mutation(s): 0  Gene Names: yutF, BSU32290 EC: 3.1.3.5
UniProt
Find proteins for O32125 (Bacillus subtilis (strain 168)) Explore O32125  Go to UniProtKB:  O32125

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.211 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.19	α = 90
b = 38.878	β = 93.04
c = 81.031	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references