3K4I | pdb_00003k4i

CRYSTAL STRUCTURE OF uncharacterized protein PSPTO_3204 from Pseudomonas syringae pv. tomato str. DC3000

• PDB DOI: https://doi.org/10.2210/pdb3K4I/pdb

• Classification: structural genomics, unknown function
• Organism(s): Pseudomonas syringae pv. tomato
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-05 Released: 2009-10-13 
• Deposition Author(s): Malashkevich, V.N., 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: 1.69 Å
• R-Value Free: 
  0.214 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

CRYSTAL STRUCTURE OF uncharacterized protein PSPTO_3204 from Pseudomonas syringae pv. tomato str. DC3000

Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 79.81 kDa 
• Atom Count: 4,974 
• Modeled Residue Count: 615 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B, C	244	Pseudomonas syringae pv. tomato	Mutation(s): 0  Gene Names: AAO56687.1, PSPTO3204
UniProt
Find proteins for Q880F6 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q880F6  Go to UniProtKB:  Q880F6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], G [auth B], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], F [auth B], H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.214 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.442	α = 90
b = 124.857	β = 97.99
c = 66.912	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Malashkevich, V.N., 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: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2012-10-24
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-10-30
  Changes: Data collection, Database references, Structure summary