3Q34 | pdb_00003q34

The crystal structure of YceI-like family protein from Pseudomonas syringae

• PDB DOI: https://doi.org/10.2210/pdb3Q34/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pseudomonas savastanoi pv. phaseolicola 1448A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2010-12-21 Released: 2011-02-23 
• Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.207 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

The crystal structure of YceI-like family protein from Pseudomonas syringae

Zhang, Z., Burley, S.K., Swaminathan, S.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.19 kDa 
• Atom Count: 6,225 
• Modeled Residue Count: 688 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YceI-like family protein	A, B, C, D	184	Pseudomonas savastanoi pv. phaseolicola 1448A	Mutation(s): 0  Gene Names: PSPPH_4050 Membrane Entity: Yes
UniProt
Find proteins for Q48EL2 (Pseudomonas savastanoi pv. phaseolicola (strain 1448A / Race 6)) Explore Q48EL2  Go to UniProtKB:  Q48EL2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UQ8	E [auth A], G [auth B], I [auth C], J [auth D]	Ubiquinone-8 C49 H74 O4 ICFIZJQGJAJRSU-SGHXUWJISA-N
GOL	F [auth A], H [auth B], K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	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:  0.207 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.647	α = 90
b = 103.357	β = 109.04
c = 63.193	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary