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- PDB-1sz2: Crystal structure of E. coli glucokinase in complex with glucose -

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Basic information

Entry
Database: PDB / ID: 1sz2
TitleCrystal structure of E. coli glucokinase in complex with glucose
ComponentsGlucokinase
KeywordsTRANSFERASE / glucokinase / ATP-dependent / glucose binding
Function / homology
Function and homology information


glucokinase / glucokinase activity / 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
beta-D-glucopyranose / Glucokinase / Glucokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLunin, V.V. / Li, Y. / Schrag, J.D. / Iannuzzi, P. / Matte, A. / Cygler, M.
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
DepositionApr 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucokinase
B: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8644
Polymers72,5032
Non-polymers3602
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-12 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.416, 53.538, 90.903
Angle α, β, γ (deg.)90.00, 112.99, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the dimer in the asymmetric unit

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Components

#1: Protein Glucokinase / / Glucose kinase


Mass: 36251.605 Da / Num. of mol.: 2 / Fragment: glucokinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLK, B2388, Z3654, ECS3268 / Plasmid: pFO4 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6V8, UniProt: P0A6V9*PLUS, glucokinase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.4 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6000, MgCl2, Tris-HCl buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 31835 / Num. obs: 31835 / % possible obs: 89.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.051 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.171 / % possible all: 63.4

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
HKL-2000data reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q18

1q18


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.87 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26511 1606 5 %RANDOM
Rwork0.19341 ---
all0.19689 35616 --
obs0.19689 30259 89.49 %-
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: 48.241 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å2-0.17 Å2
2--1.14 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4922 0 24 348 5294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215052
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9636838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51423.333213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.36515851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5441533
X-RAY DIFFRACTIONr_chiral_restr0.1170.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023775
X-RAY DIFFRACTIONr_nbd_refined0.2280.22447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2366
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6910.216
X-RAY DIFFRACTIONr_mcbond_it0.9331.53159
X-RAY DIFFRACTIONr_mcangle_it1.73625061
X-RAY DIFFRACTIONr_scbond_it2.41631893
X-RAY DIFFRACTIONr_scangle_it3.8964.51777
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 85
Rwork0.21 1516

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