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- PDB-9duc: Wild-Type E. coli Glucokinase -

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Basic information

Entry
Database: PDB / ID: 9duc
TitleWild-Type E. coli Glucokinase
ComponentsGlucokinase
KeywordsTRANSFERASE / metabolic role
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
PHOSPHATE ION / Glucokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsAndrews, J.R.W. / Fan, C. / Sakon, J.
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 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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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)71,3804
Polymers71,1902
Non-polymers1902
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-26 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.106, 82.106, 237.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris HCl/ Sodium hydroxide pH 8.5, 200 mM Lithium sulfate, 20% (w/v) PEG 5000mME

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.63→29.74 Å / Num. obs: 25056 / % possible obs: 99.8 % / Redundancy: 9.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.072 / Rrim(I) all: 0.228 / Χ2: 0.95 / Net I/σ(I): 9.2 / % possible anomalous: 99.9 / Redundancy anomalous: 5.2
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
2.63-2.7610.70.93132660.7430.3040.980.933.71005.5100
8.72-29.745.80.0697430.9940.0290.0750.7415.996.73.593

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→29.74 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 0.02 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 1228 5.03 %
Rwork0.191 --
obs0.193 24428 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 10 114 4998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024997
X-RAY DIFFRACTIONf_angle_d0.5046769
X-RAY DIFFRACTIONf_dihedral_angle_d4.335687
X-RAY DIFFRACTIONf_chiral_restr0.042759
X-RAY DIFFRACTIONf_plane_restr0.004874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.740.3361280.26572461X-RAY DIFFRACTION95
2.74-2.860.31311250.25912456X-RAY DIFFRACTION95
2.86-3.010.28641320.25272491X-RAY DIFFRACTION96
3.01-3.20.23771340.22922504X-RAY DIFFRACTION96
3.2-3.450.25671390.20372575X-RAY DIFFRACTION98
3.45-3.790.24841370.1832583X-RAY DIFFRACTION99
3.79-4.340.19881420.16592647X-RAY DIFFRACTION99
4.34-5.460.19051420.15152675X-RAY DIFFRACTION99
5.46-29.740.19111490.16882808X-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)
15.1901-0.06940.37342.4975-0.1884.86650.19250.7087-0.0541-0.3989-0.0556-0.06750.1780.1097-0.09740.2540.00430.02420.2694-0.05230.2511-28.6698-34.980615.9824
22.26561.03981.17872.060.84512.17750.02780.0791-0.17550.19170.0375-0.28980.34450.1259-0.02270.16530.02530.03220.2027-0.04140.2499-17.1062-28.235133.6563
31.8514-0.3897-0.51582.5642-1.66512.96360.08390.13660.1302-0.0219-0.04060.1152-0.3615-0.1859-0.02660.17210.033-0.02130.2284-0.03530.1962-16.2741-5.379729.9109
41.97291.27651.06313.53841.75553.47640.03190.1393-0.19210.24520.1847-0.34510.36010.4828-0.14240.15280.06390.00080.2342-0.01160.2752-14.238-27.750234.4668
55.8605-0.0529-0.21233.53141.50574.9696-0.0613-0.424-0.23990.3805-0.01760.04910.4913-0.0195-0.00370.3073-0.0820.08660.32580.01950.3094-24.6194-31.701874.2143
67.0541-0.6569-0.56998.6819-2.69646.7043-0.294-0.65350.56310.41290.5737-0.4866-0.20430.7659-0.18230.353-0.02590.01980.5057-0.08970.5726-12.2759-27.183468.6026
71.79430.0735-0.49261.8004-0.6212.85950.0379-0.23280.1090.2549-0.05470.2593-0.5281-0.39940.0420.30940.07250.04420.4786-0.06280.218-27.5249-10.957254.2984
81.7534-0.0062-0.06511.6016-0.79372.59460.0423-0.18230.16360.24540.06450.5314-0.2374-0.83260.02810.22530.09090.0770.5604-0.08420.3198-34.1736-15.296951.5905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 155 )
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 284 )
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 321 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 63 )
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 93 )
7X-RAY DIFFRACTION7chain 'B' and (resid 94 through 227 )
8X-RAY DIFFRACTION8chain 'B' and (resid 228 through 321 )

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