3KSM | pdb_00003ksm

Crystal structure of ABC-type sugar transport system, periplasmic component from Hahella chejuensis

• PDB DOI: https://doi.org/10.2210/pdb3KSM/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Hahella chejuensis KCTC 2396
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-23 Released: 2009-12-15 
• Deposition Author(s): Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of ABC-type sugar transport system, periplasmic component from Hahella chejuensis

Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.53 kDa 
• Atom Count: 4,585 
• Modeled Residue Count: 550 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type sugar transport system, periplasmic component	A, B	276	Hahella chejuensis KCTC 2396	Mutation(s): 0  Gene Names: HCH_06819
UniProt
Find proteins for Q2S7D2 (Hahella chejuensis (strain KCTC 2396)) Explore Q2S7D2  Go to UniProtKB:  Q2S7D2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDR	C [auth A], D [auth B]	beta-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-TXICZTDVSA-N

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: 1.90 Å
• R-Value Free:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.439	α = 103.49
b = 47.712	β = 90.49
c = 79.723	γ = 91.06

Software Package:

Software Name	Purpose
CBASS	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-15 
Deposition Author(s): Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-02-10
  Changes: Database references, Structure summary
• Version 2.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary