3BDD | pdb_00003bdd

CRYSTAL STRUCTURE OF A PUTATIVE MULTIPLE ANTIBIOTIC-RESISTANCE REPRESSOR (SSU05_1136) FROM STREPTOCOCCUS SUIS 89/1591 AT 2.20 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3BDD/pdb

• Classification: TRANSCRIPTION
• Organism(s): Streptococcus suis 89/1591
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-14 Released: 2007-12-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.275 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Crystal structure of putative multiple antibiotic-resistance repressor (MarR) (ZP_00875883.1) from Streptococcus suis 89/1591 at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.55 kDa 
• Atom Count: 4,630 
• Modeled Residue Count: 545 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein MarR	A, B, C, D	142	Streptococcus suis 89/1591	Mutation(s): 0  Gene Names: ZP_00875883.1, SsuiDRAFT_0346

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth A], H [auth B], I [auth C], J [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: 2.20 Å
• R-Value Free:  0.275 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33BDD

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.734	α = 90
b = 100.43	β = 111.42
c = 68.695	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary