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- PDB-9dvz: Wild-Type E. coli Glucokinase with Glucose bound -

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Basic information

Entry
Database: PDB / ID: 9dvz
TitleWild-Type E. coli Glucokinase with Glucose bound
ComponentsGlucokinase
KeywordsTRANSFERASE/SUBSTRATE / binding properties / TRANSFERASE / TRANSFERASE-SUBSTRATE complex
Function / homology
Function and homology information


glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATP binding / cytosol
Similarity search - Function
: / Glucokinase / Glucokinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
beta-D-glucopyranose / PHOSPHATE ION / Glucokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsAndrews, J.R.W. / Sakon, J. / Fan, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM140433 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM139768 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Crystal structures of Escherichia coli glucokinase and insights into phosphate binding.
Authors: Andrews, J. / Sakon, J. / Fan, C.
History
DepositionOct 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 22, 2025Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID / _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucokinase
B: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7406
Polymers71,1902
Non-polymers5504
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-25 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.535, 66.284, 207.527
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 Glucokinase / Glucose kinase


Mass: 35594.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glk, EcE24377A_2678 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7ZPJ8, glucokinase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 46.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.46
Details: 100 mM Bis-Tris / Hydrochloric acid pH 6.5, 200 mM Magnesium chloride, and 23% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.54→22.72 Å / Num. obs: 22445 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.983 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.107 / Rrim(I) all: 0.243 / Χ2: 0.92 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2Net I/σ(I) obs% possible anomalousRedundancy anomalous% possible all
2.54-2.655.30.59227080.8020.2820.6570.962.61002.6100
8.78-22.722.80.0695500.9950.0460.0830.757.769.61.689.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→22.72 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 1090 4.87 %
Rwork0.2032 --
obs0.2061 22385 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→22.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 34 171 5065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025021
X-RAY DIFFRACTIONf_angle_d0.5416808
X-RAY DIFFRACTIONf_dihedral_angle_d4.597690
X-RAY DIFFRACTIONf_chiral_restr0.044771
X-RAY DIFFRACTIONf_plane_restr0.004874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.660.32371290.25452640X-RAY DIFFRACTION100
2.66-2.80.28231460.2262586X-RAY DIFFRACTION100
2.8-2.970.29771400.22872634X-RAY DIFFRACTION100
2.97-3.20.30451310.21972630X-RAY DIFFRACTION100
3.2-3.520.26031250.19092658X-RAY DIFFRACTION100
3.52-4.030.24121290.17912677X-RAY DIFFRACTION100
4.03-5.070.22681470.17382690X-RAY DIFFRACTION100
5.07-22.720.22471430.20582780X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8029-0.3248-0.19122.2966-0.28711.2010.19810.17310.64880.02040.17950.5869-0.8099-0.5731-0.09360.38890.09440.00070.250.10750.4684-12.493530.587-36.9379
22.5766-0.32121.07430.8137-0.18231.3187-0.00460.06610.2818-0.11780.03240.2322-0.1122-0.26670.03290.13090.0293-0.09530.17840.08070.2317-7.055918.364-32.8436
31.1224-0.2256-0.05841.09320.15032.05840.0357-0.12020.0750.0830.06280.002-0.18580.0030.01250.0550.0137-0.05730.08780.05720.08520.523816.2433-13.0862
40.8461-0.3290.63460.80890.17640.9178-0.02540.10710.0969-0.1723-0.0595-0.0224-0.16270.1350.31530.0799-0.0315-0.04140.11760.03870.10076.827414.3979-28.2533
51.1180.479-0.29531.8853-0.09621.34760.0421-0.0108-0.56230.0433-0.0589-0.42890.60520.40940.0240.31240.0864-0.06930.2131-0.01580.455215.0408-19.7589-35.5708
62.336-0.2531-0.14020.85470.31151.1426-0.0570.4018-0.0864-0.22450.0520.0890.0257-0.1608-0.05880.1207-0.0365-0.06760.10010.03530.11-2.9851-8.157-32.7268
70.3676-0.0210.05880.62140.12080.68930.0664-0.1689-0.19640.19180.02720.02130.3132-0.0034-0.10530.16770.0012-0.09170.13240.18750.1475-1.7988-10.1646-9.8691
81.3613-0.4956-1.24471.14151.04511.80890.04590.1086-0.2243-0.1233-0.12760.09680.0628-0.18910.08120.1040.0249-0.07690.1330.00510.2003-5.9999-7.549-30.6391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 274 )
4X-RAY DIFFRACTION4chain 'A' and (resid 275 through 321 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 93 )
6X-RAY DIFFRACTION6chain 'B' and (resid 94 through 154 )
7X-RAY DIFFRACTION7chain 'B' and (resid 155 through 281 )
8X-RAY DIFFRACTION8chain 'B' and (resid 282 through 321 )

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