3E61 | pdb_00003e61

Crystal structure of a putative transcriptional repressor of ribose operon from Staphylococcus saprophyticus subsp. saprophyticus

• PDB DOI: https://doi.org/10.2210/pdb3E61/pdb

• Classification: structural genomics, unknown function
• Organism(s): Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-14 Released: 2008-08-26 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Romero, R., Smith, D., Wasserman, S., 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: 2.00 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal structure of a putative transcriptional repressor of ribose operon from Staphylococcus saprophyticus subsp. saprophyticus

Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 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: 62.94 kDa 
• Atom Count: 3,822 
• Modeled Residue Count: 480 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional repressor of ribose operon	A, B	277	Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292	Mutation(s): 0  Gene Names: SSP1396
UniProt
Find proteins for Q49XF6 (Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229 / NCIMB 8711 / NCTC 7292 / S-41)) Explore Q49XF6  Go to UniProtKB:  Q49XF6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.146	α = 90
b = 106.634	β = 112.17
c = 68.183	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references