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- PDB-1gc5: CRYSTAL STRUCTURE OF A NOVEL ADP-DEPENDENT GLUCOKINASE FROM THERM... -

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Basic information

Entry
Database: PDB / ID: 1gc5
TitleCRYSTAL STRUCTURE OF A NOVEL ADP-DEPENDENT GLUCOKINASE FROM THERMOCOCCUS LITORALIS
ComponentsADP-DEPENDENT GLUCOKINASEADP-specific glucokinase
KeywordsTRANSFERASE / ALFA/BETA SANDWICHS / INDUCED-FITTING
Function / homology
Function and homology information


ADP-specific glucose/glucosamine kinase / ADP-specific glucokinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / glucokinase activity / glycolytic process / glucose metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
ADP-dependent glucose/glucosamine kinase, archaeal / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...ADP-dependent glucose/glucosamine kinase, archaeal / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADP-dependent glucose/glucosamine kinase
Similarity search - Component
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsIto, S. / Fushinobu, S. / Yoshioka, I. / Koga, S. / Matsuzawa, H. / Wakagi, T.
CitationJournal: Structure / Year: 2001
Title: Structural Basis for the ADP-Specificity of a Novel Glucokinase from a Hyperthermophilic Archaeon
Authors: Ito, S. / Fushinobu, S. / Yoshioka, I. / Koga, S. / Matsuzawa, H. / Wakagi, T.
History
DepositionJul 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-DEPENDENT GLUCOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0452
Polymers53,6181
Non-polymers4271
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.8, 109.8, 129.8
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is monomer.

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Components

#1: Protein ADP-DEPENDENT GLUCOKINASE / ADP-specific glucokinase


Mass: 53618.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus litoralis (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: Q7M537, ADP-specific glucose/glucosamine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.21 Å3/Da / Density % sol: 70.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: potassium chloride, citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
21.8-2.0 M1reservoirNaCl
3100 mMsodium citrate1reservoir
42 mMADP1reservoir
510 mM1reservoirMg2+

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 167633 / Num. obs: 46477 / % possible obs: 77 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.6
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.177 / % possible all: 45.8
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 77 % / Num. measured all: 167633

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
X-PLOR3.851refinement
RefinementResolution: 2.3→6 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.252 1500 RANDOM
Rwork0.204 --
obs-30940 -
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 27 77 3884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.414
X-RAY DIFFRACTIONo_bond_d0.008
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg

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