2PFX | pdb_00002pfx

Crystal structure of uncharacterized peroxidase-related protein (YP_614459.1) from Silicibacter sp. TM1040 at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PFX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ruegeria sp. TM1040
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-05 Released: 2007-04-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.120 (DCC) 
• R-Value Observed: 
  0.114 (Depositor) 

Literature

Crystal structure of uncharacterized peroxidase-related protein (YP_614459.1) from Silicibacter sp. TM1040 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 44.57 kDa 
• Atom Count: 3,384 
• Modeled Residue Count: 382 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized peroxidase-related protein	A, B	191	Ruegeria sp. TM1040	Mutation(s): 13  Gene Names: YP_614459.1, TM1040_2465

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ACT	C [auth A], E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.120 (DCC) 
• R-Value Observed: 0.114 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32PFX

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.069	α = 90
b = 85.069	β = 90
c = 105.616	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
SOLVE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-04-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-11-06
  Changes: Data collection, Structure summary