2D62 | pdb_00002d62

Crystal structure of multiple sugar binding transport ATP-binding protein

• PDB DOI: https://doi.org/10.2210/pdb2D62/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-08 Released: 2006-05-08 
• Deposition Author(s): Lokanath, N.K., Mizohata, E., Yamaguchi-Sihta, E., Chen, L., Liu, Z.J., Wang, B.C., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal structure of multiple sugar binding transport ATP-binding protein

Lokanath, N.K., Mizohata, E., Yamaguchi-Sihta, E., Chen, L., Liu, Z.J., Wang, B.C., Kunishima, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.08 kDa 
• Atom Count: 3,369 
• Modeled Residue Count: 375 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
multiple sugar-binding transport ATP-binding protein	A	375	Pyrococcus horikoshii	Mutation(s): 14
UniProt
Find proteins for O57933 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57933  Go to UniProtKB:  O57933

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP	I [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.10 Å
• R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.304	α = 90
b = 119.304	β = 90
c = 180.503	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-08 
Deposition Author(s): Lokanath, N.K., Mizohata, E., Yamaguchi-Sihta, E., Chen, L., Liu, Z.J., Wang, B.C., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-05-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary