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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.212 (Depositor), 0.226 (DCC)
R-Value Work:
0.183 (Depositor), 0.195 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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This is version 1.6 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4K6H7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.226 (DCC)
R-Value Work: 0.183 (Depositor), 0.195 (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

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Entry History

Deposition Data

Released Date: 2010-03-23

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.