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- PDB-1q18: Crystal structure of E.coli glucokinase (Glk) -

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Basic information

Entry
Database: PDB / ID: 1q18
TitleCrystal structure of E.coli glucokinase (Glk)
ComponentsGlucokinase
KeywordsTRANSFERASE / glucokinase / ATP / kinase / phosphotransfer / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATP binding / cytosol / cytoplasm
Similarity search - Function
: / Glucokinase / Glucokinase / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucokinase / Glucokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.36 Å
AuthorsLunin, V.V. / Li, Y. / Schrag, J.D. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Bacteriol. / Year: 2004
Title: Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose.
Authors: Lunin, V.V. / Li, Y. / Schrag, J.D. / Iannuzzi, P. / Cygler, M. / Matte, A.
History
DepositionJul 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucokinase
B: Glucokinase


Theoretical massNumber of molelcules
Total (without water)72,5032
Polymers72,5032
Non-polymers00
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-18 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.474, 81.474, 234.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsthe biological unit is a dimer

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Components

#1: Protein Glucokinase / Glucose kinase


Mass: 36251.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLK OR B2388 OR Z3654 OR ECS3268 / Plasmid: pFO4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A6V8, UniProt: P0A6V9*PLUS, glucokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 4000, 0.1M Tris-HCl, 0.2M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.964711, 0.979962, 0.980178
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9647111
20.9799621
30.9801781
ReflectionResolution: 2.36→19.76 Å / Num. all: 30408 / Num. obs: 30408 / % possible obs: 95.83 % / Observed criterion σ(I): 0 / Rsym value: 0.046

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.36→19.76 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.238 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.375 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1657 5.2 %RANDOM
Rwork0.20619 ---
all0.20931 ---
obs0.20931 30408 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.389 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.36→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4908 0 0 387 5295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214994
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9576765
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023768
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.22487
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2366
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6061.53161
X-RAY DIFFRACTIONr_mcangle_it1.15625055
X-RAY DIFFRACTIONr_scbond_it1.64831833
X-RAY DIFFRACTIONr_scangle_it2.7044.51710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.36→2.42 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 117
Rwork0.218 2029

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