3G1P | pdb_00003g1p

Crystals structure of PhnP from E.coli K-12

• PDB DOI: https://doi.org/10.2210/pdb3G1P/pdb

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


• Deposited: 2009-01-30 Released: 2009-03-03 
• Deposition Author(s): Podzelinska, K., Jia, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystals structure of PhnP from E.coli K-12

Podzelinska, K., He, S., Wathier, M., Yakunin, A., Proudftoot, M., Hove-Jensen, B., Zechel, D., 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: 58.03 kDa 
• Atom Count: 4,789 
• 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
MLT	F [auth A], J [auth B]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
ZN	C [auth A], G [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: 1.40 Å
• R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.65	α = 90
b = 75.405	β = 126.33
c = 83.228	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
autoSHARP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Podzelinska, K., Jia, Z.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations