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- PDB-8dtc: Crystal Structure of Glucokinase with bound glucose from Acantham... -

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Basic information

Entry
Database: PDB / ID: 8dtc
TitleCrystal Structure of Glucokinase with bound glucose from Acanthamoeba castellanii
ComponentsGlucokinase
KeywordsTRANSFERASE / SSGCID / ATP binding / glucokinase / glucose binding / glycolytic process / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyGlucokinase / Glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATPase, nucleotide binding domain / ATP binding / beta-D-glucopyranose / Glucokinase
Function and homology information
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of Glucokinase with bound glucose from Acanthamoeba castellanii
Authors: DeBouver, N.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)88,94610
Polymers87,9092
Non-polymers1,0378
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-22 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.990, 52.790, 118.350
Angle α, β, γ (deg.)90.000, 118.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucokinase /


Mass: 43954.570 Da / Num. of mol.: 2 / Fragment: AccaA.19900.a.Q2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Gene: ACA1_177380 / Plasmid: AccaA.19900.a.Q2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L8GT25
#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.: 4 / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.59 Å3/Da / Density % sol: 65.71 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: AccaA.19900.a.Q2.PS38640 at 25.33 mg/mL was mixed 1:1 (0.2 uL protein and 0.2 uL precipitant) with 0.1 M MES: NaOH, pH 6.5, 1.6 M Magnesium Sulfate (MCSG-1 E5). [Barcode: 321398e5] [pin: ...Details: AccaA.19900.a.Q2.PS38640 at 25.33 mg/mL was mixed 1:1 (0.2 uL protein and 0.2 uL precipitant) with 0.1 M MES: NaOH, pH 6.5, 1.6 M Magnesium Sulfate (MCSG-1 E5). [Barcode: 321398e5] [pin: bzu2-8] [cryo: 20% Ethylene glycol]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 1, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.25→39.38 Å / Num. obs: 59214 / % possible obs: 98.7 % / Redundancy: 3.75 % / Biso Wilson estimate: 32.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.093 / Χ2: 0.914 / Net I/σ(I): 12.35 / Num. measured all: 222043 / Scaling rejects: 141
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.3950.5222.2914974443244100.7370.61899.5
2.31-2.373.7820.462.7816061425642470.8030.53699.8
2.37-2.443.7840.3813.4315755418241640.8530.44399.6
2.44-2.523.8080.3214.0315433406840530.8970.37499.6
2.52-2.63.7990.2814.614728389338770.9170.32799.6
2.6-2.693.8010.2155.8214383380937840.9470.2599.3
2.69-2.793.8050.1797.0113973369536720.9630.20899.4
2.79-2.93.8020.1478.5213276351834920.9760.17199.3
2.9-3.033.810.11610.6312786338633560.9850.13599.1
3.03-3.183.810.09712.7812259325332180.9880.11398.9
3.18-3.353.8050.08115.2911585308530450.9920.09498.7
3.35-3.563.7710.06119.4610891292928880.9940.07198.6
3.56-3.83.7480.05222.810285279127440.9960.0698.3
3.8-4.113.7170.04625.949374258125220.9960.05397.7
4.11-4.53.7150.04326.898541235522990.9970.0597.6
4.5-5.033.750.03727.797882216121020.9980.04497.3
5.03-5.813.7590.03927.17040193018730.9980.04597
5.81-7.123.7680.03827.455890161815630.9980.04596.6
7.12-10.063.7080.03131.844557129012290.9980.03695.3
10.06-39.383.5060.0334.1523707476760.9980.03590.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.25→39.38 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 2067 3.49 %
Rwork0.1694 57141 -
obs0.1705 59208 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.31 Å2 / Biso mean: 40.5027 Å2 / Biso min: 16.52 Å2
Refinement stepCycle: final / Resolution: 2.25→39.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5755 0 66 558 6379
Biso mean--46.2 45.17 -
Num. residues----748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.30.25491450.223738503995100
2.3-2.360.27471330.222437643897100
2.36-2.420.23541240.212538333957100
2.42-2.490.26091410.196238103951100
2.5-2.580.23011420.197737933935100
2.58-2.670.20971260.18738033929100
2.67-2.770.24691670.19023815398299
2.77-2.90.22861280.18033803393199
2.9-3.050.23321540.18053786394099
3.05-3.240.18861150.17333850396599
3.24-3.50.23131250.16973807393299
3.5-3.850.18181550.15453779393499
3.85-4.40.18451840.13993756394098
4.4-5.540.14621420.1393774391697
5.54-39.380.1581860.16653918400496
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)
12.65880.86751.84233.43631.40556.85630.02460.6008-0.1029-0.8150.14950.00780.20110.1828-0.0820.7567-0.0014-0.07040.34180.00310.24913.05931.3389-5.9201
21.4865-0.24610.30711.7991-0.52923.9355-0.07330.1442-0.0157-0.35420.02280.0015-0.03010.09230.05690.30120.01580.00530.1991-0.03460.19346.43863.324912.7951
33.0819-0.2630.22441.53230.18412.01040.0771-0.0276-0.1539-0.1448-0.1531-0.2580.10940.50370.06820.21840.03080.02230.34190.05620.193121.5311-2.564532.7203
41.9919-0.10490.2721.3215-0.05921.84180.01050.0434-0.237-0.3079-0.0683-0.06760.44290.32260.07430.29520.05280.03850.2388-0.01740.274712.0718-10.684727.0169
54.51240.4029-1.22327.16090.1572.48690.0403-0.56760.57930.5347-0.18950.0450.0446-0.02370.18120.2901-0.02250.14060.21990.01570.4574-32.4232-1.24957.2645
64.48050.4328-1.04562.62460.20682.22180.0913-0.37540.07950.1471-0.01370.08510.00360.078-0.00010.1825-0.0180.02740.1239-0.02250.2282-20.6311-5.783555.6427
75.24011.6165-1.08153.49320.62862.61770.1488-0.1512-1.18910.2465-0.0595-0.39770.68720.53420.08080.25390.0410.01110.26990.02160.4936-3.9108-13.745450.3673
82.6410.2491-0.45740.72460.0561.04050.0963-0.03430.02620.0353-0.0611-0.03-0.10330.2024-0.03790.2148-0.0290.01450.2024-0.010.2078-0.17052.88245.8286
91.5783-0.45320.04822.69410.72862.51220.048-0.76010.1930.8036-0.23530.03930.33680.00950.09760.3925-0.16150.03470.5905-0.04480.252511.20588.064461.6958
102.36170.5135-0.47721.32440.21371.54510.1885-0.34390.27080.1831-0.04860.1232-0.1450.2362-0.12730.2064-0.01550.01160.1908-0.0290.2179-0.115911.920647.1431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 33 )A12 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 182 )A34 - 182
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 320 )A183 - 320
4X-RAY DIFFRACTION4chain 'A' and (resid 321 through 385 )A321 - 385
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 33 )B12 - 33
6X-RAY DIFFRACTION6chain 'B' and (resid 34 through 100 )B34 - 100
7X-RAY DIFFRACTION7chain 'B' and (resid 101 through 126 )B101 - 126
8X-RAY DIFFRACTION8chain 'B' and (resid 127 through 258 )B127 - 258
9X-RAY DIFFRACTION9chain 'B' and (resid 259 through 319 )B259 - 319
10X-RAY DIFFRACTION10chain 'B' and (resid 320 through 385 )B320 - 385

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