3MCP | pdb_00003mcp

Crystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3MCP/pdb

• Classification: TRANSFERASE
• Organism(s): Parabacteroides distasonis ATCC 8503
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-29 Released: 2010-05-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.53 kDa 
• Atom Count: 2,618 
• Modeled Residue Count: 355 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	366	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_1628
UniProt
Find proteins for A6LCG6 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LCG6  Go to UniProtKB:  A6LCG6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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: 3.00 Å
• R-Value Free:  0.249 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33MCP

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.732	α = 90
b = 80.732	β = 90
c = 142.581	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary