3P2U | pdb_00003p2u

Crystal structure of PhnP in complex with orthovanadate

• PDB DOI: https://doi.org/10.2210/pdb3P2U/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-10-04 Released: 2011-01-05 
• Deposition Author(s): Podzelinska, K., Kim, Y.M., Zechel, D., Faucher, F., Jia, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.186 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Crystal structure of PhnP in complex with orthovanadate

Podzelinska, K., Kim, Y.M., Zechel, D., Faucher, F., Jia, Z.

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: 57.99 kDa 
• Atom Count: 4,580 
• Modeled Residue Count: 499 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein phnP	A, B	258	Escherichia coli K-12	Mutation(s): 0  Gene Names: b4092, JW4053, phnP EC: 3.1.4.55
UniProt
Find proteins for P16692 (Escherichia coli (strain K12)) Explore P16692  Go to UniProtKB:  P16692

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VO4	C [auth A], G [auth B]	VANADATE ION O4 V LSGOVYNHVSXFFJ-UHFFFAOYSA-N
ZN	F [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN	D [auth A], E [auth A], H [auth B], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.186 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.761	α = 90
b = 75.285	β = 125.52
c = 82.423	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-05 
Deposition Author(s): Podzelinska, K., Kim, Y.M., Zechel, D., Faucher, F., Jia, Z.

Revision History  

• Version 1.0: 2011-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.3: 2024-02-21
  Changes: Advisory, Data collection, Database references, Derived calculations