3D02 | pdb_00003d02

Crystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3D02/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-30 Released: 2008-05-27 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.172 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Crystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.66 kDa 
• Atom Count: 2,925 
• Modeled Residue Count: 300 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative LACI-type transcriptional regulator	A	303	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: YP_001338366.1, KPN78578_46750, KPN_04753
UniProt
Find proteins for A6THR5 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6THR5  Go to UniProtKB:  A6THR5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.172 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33D02

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.24	α = 90
b = 76.96	β = 90
c = 113.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary