3LYP | pdb_00003lyp

Structure of stringent starvation protein A homolog from Pseudomonas fluorescens

• PDB DOI: https://doi.org/10.2210/pdb3LYP/pdb

• Classification: TRANSCRIPTION
• Organism(s): Pseudomonas protegens Pf-5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-28 Released: 2010-03-23 
• Deposition Author(s): Ramagopal, U.A., Toro, R., 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: 1.60 Å
• R-Value Free: 
  0.212 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Structure of stringent starvation protein A homolog from Pseudomonas fluorescens

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

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: 49.67 kDa 
• Atom Count: 3,500 
• Modeled Residue Count: 393 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stringent starvation protein A	A, B	215	Pseudomonas protegens Pf-5	Mutation(s): 0  Gene Names: PFL_5077, sspA
UniProt
Find proteins for Q4K6H7 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4K6H7  Go to UniProtKB:  Q4K6H7

Small Molecules

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: 1.60 Å
• R-Value Free:  0.212 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.591	α = 85.28
b = 53.917	β = 71.05
c = 54.496	γ = 66.71

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection
• Version 1.6: 2024-11-27
  Changes: Structure summary