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- PDB-1l2l: Crystal structure of ADP-dependent glucokinase from a Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 1l2l
TitleCrystal structure of ADP-dependent glucokinase from a Pyrococcus Horikoshii
ComponentsADP-dependent GlucokinaseADP-specific glucokinase
KeywordsTRANSFERASE / ADP glucokinase apo
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
ADP-dependent glucose/glucosamine kinase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsTsuge, H. / Sakuraba, H. / Katunuma, N. / Ohshima, T.
CitationJournal: PROTEIN SCI. / Year: 2002
Title: Crystal structure of the ADP-dependent glucokinase from Pyrococcus horikoshii at 2.0-A resolution: a large conformational change in ADP-dependent glucokinase
Authors: Tsuge, H. / Sakuraba, H. / Kobe, T. / Kujime, A. / Katunuma, N. / Ohshima, T.
History
DepositionFeb 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-dependent Glucokinase


Theoretical massNumber of molelcules
Total (without water)52,1661
Polymers52,1661
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.760, 74.730, 99.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-dependent Glucokinase / ADP-specific glucokinase


Mass: 52166.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O58328, glucokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: PEG6000, LiSO4, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
29-13 %PEG60001reservoir
30.2 M1reservoirLi2SO4
40.1 Mcitrate1reservoirpH3.6

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 32198 / Num. obs: 25645 / % possible obs: 97 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.178 / Num. unique all: 1660 / % possible all: 80
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. obs: 275056 / % possible obs: 99.1 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Lowest resolution: 2.11 Å / % possible obs: 97.1 % / Rmerge(I) obs: 0.418

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→14.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 266483.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2911 10.1 %RANDOM
Rwork0.213 ---
obs0.213 28958 87.2 %-
all-32198 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9668 Å2 / ksol: 0.368907 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.39 Å20 Å20 Å2
2---8.21 Å20 Å2
3---12.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 0 394 3873
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.352
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 296 9.3 %
Rwork0.247 2889 -
obs--58.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Rfactor Rfree: 0.28 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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