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- PDB-5o5x: Crystal structure of Thermococcus litoralis ADP-dependent glucoki... -

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Basic information

Entry
Database: PDB / ID: 5o5x
TitleCrystal structure of Thermococcus litoralis ADP-dependent glucokinase (GK)
ComponentsADP-dependent glucokinase,ADP-dependent glucokinase,ADP-dependent glucokinase
KeywordsTRANSFERASE / ADP-DEPENDENT / GLUCOKINASE / RIBOKINASE SUPERFAMILY
Function / homology
Function and homology information


ADP-specific glucose/glucosamine kinase / ADP-specific glucokinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / glucokinase activity / glycolytic process / glucose metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
ADP-dependent glucose/glucosamine kinase, archaeal / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Ribokinase-like
Similarity search - Domain/homology
ADP-dependent glucose/glucosamine kinase
Similarity search - Component
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å
AuthorsHerrera-Morande, A. / Castro-Fernandez, V. / Merino, F. / Ramirez-Sarmiento, C.A. / Fernandez, F.J. / Guixe, V. / Vega, M.C.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessCTQ2015-66206-C2-2-R Spain
Spanish National Research CouncilPIE-201620E064 Spain
Citation
Journal: Biochim Biophys Acta Gen Subj / Year: 2018
Title: Protein topology determines substrate-binding mechanism in homologous enzymes.
Authors: Herrera-Morande, A. / Castro-Fernandez, V. / Merino, F. / Ramirez-Sarmiento, C.A. / Fernandez, F.J. / Vega, M.C. / Guixe, V.
#1: Journal: PLoS ONE / Year: 2013
Title: Crystal structure, SAXS and kinetic mechanism of hyperthermophilic ADP-dependent glucokinase from Thermococcus litoralis reveal a conserved mechanism for catalysis.
Authors: Rivas-Pardo, J.A. / Herrera-Morande, A. / Castro-Fernandez, V. / Fernandez, F.J. / Vega, M.C. / Guixe, V.
History
DepositionJun 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-dependent glucokinase,ADP-dependent glucokinase,ADP-dependent glucokinase
B: ADP-dependent glucokinase,ADP-dependent glucokinase,ADP-dependent glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,97319
Polymers105,3842
Non-polymers1,58917
Water3,711206
1
A: ADP-dependent glucokinase,ADP-dependent glucokinase,ADP-dependent glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4419
Polymers52,6921
Non-polymers7498
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-dependent glucokinase,ADP-dependent glucokinase,ADP-dependent glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,53310
Polymers52,6921
Non-polymers8419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.190, 99.270, 113.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-dependent glucokinase,ADP-dependent glucokinase,ADP-dependent glucokinase / ADPGK


Mass: 52691.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C) (archaea)
Gene: glkA, OCC_09701 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7M537, ADP-specific glucose/glucosamine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium sulfate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2013
Details: Cryogenically cooled channel cut Si[111] crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Cryogenically cooled channel-cut Si[111] monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.148→48.73 Å / Num. obs: 58644 / % possible obs: 98.88 % / Redundancy: 4.4 % / Biso Wilson estimate: 46.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0531 / Rpim(I) all: 0.0275 / Rrim(I) all: 0.06014 / Net I/σ(I): 14.24
Reflection shellResolution: 2.148→2.225 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.9124 / Num. unique obs: 5574 / CC1/2: 0.677 / Rpim(I) all: 0.4792 / Rsym value: 1.036 / % possible all: 95.59

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B8R

4b8r


Resolution: 2.148→48.729 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 2930 5 %
Rwork0.1935 55642 -
obs0.1951 58572 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.44 Å2 / Biso mean: 65.9743 Å2 / Biso min: 30.2 Å2
Refinement stepCycle: final / Resolution: 2.148→48.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7226 0 96 206 7528
Biso mean--74.48 55.25 -
Num. residues----903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037469
X-RAY DIFFRACTIONf_angle_d0.54210083
X-RAY DIFFRACTIONf_chiral_restr0.0421105
X-RAY DIFFRACTIONf_plane_restr0.0041303
X-RAY DIFFRACTIONf_dihedral_angle_d17.5974487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1485-2.18370.43921270.37322423255092
2.1837-2.22130.36621380.3232622276099
2.2213-2.26170.27931390.299426342773100
2.2617-2.30520.3581370.280826052742100
2.3052-2.35230.34211400.271126472787100
2.3523-2.40340.24391380.25472627276599
2.4034-2.45930.29191400.247226572797100
2.4593-2.52080.30591390.24252640277999
2.5208-2.5890.28621390.25142636277599
2.589-2.66520.32831370.23832595273299
2.6652-2.75120.31251410.237226812822100
2.7512-2.84950.24421390.22262642278199
2.8495-2.96360.2731390.21832649278899
2.9636-3.09840.29311410.22172665280699
3.0984-3.26180.23411400.21122658279899
3.2618-3.46610.22951400.1952659279999
3.4661-3.73360.18291400.16982659279999
3.7336-4.10920.1961410.16092695283699
4.1092-4.70330.16551420.1482685282799
4.7033-5.92410.19741440.172739288399
5.9241-48.74140.18341490.16212824297398
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)
14.0133-2.21560.66552.64960.17222.5537-0.275-0.2170.15630.34670.2017-0.1782-0.02120.22050.07580.3519-0.02390.00340.53740.05190.263367.982652.752.1821
22.1313-0.6371-0.03192.9142-0.25743.1290.12120.3453-0.0428-0.2575-0.0684-0.0104-0.01480.131-0.04280.28480.07720.02530.5068-0.00530.272664.999851.779136.1723
34.23910.8777-0.90594.0220.85294.81670.0070.30730.3962-0.4646-0.06320.1896-0.7176-0.56690.04120.41340.1579-0.04180.49160.05290.293254.87570.520345.2775
41.70480.47430.75932.593-0.79923.9536-0.0215-0.12630.429-0.0225-0.2042-0.8784-0.79360.44330.22460.64790.08430.10180.5275-0.11190.920566.983485.874188.5232
52.214-1.83370.95184.4002-0.48284.4777-0.2409-0.63720.34840.58120.31780.2393-0.5955-0.5106-0.06260.49740.18370.13140.665-0.00240.470754.731476.839291.6952
63.90110.4447-1.47513.7076-1.74125.6990.1807-0.44270.16410.0142-0.0716-0.2141-0.29540.7045-0.11090.2664-0.0267-0.00090.394-0.07510.274764.427173.838872.3695
75.99992.22930.84557.239-0.86036.78760.4965-0.14541.1446-0.1480.0149-0.1874-1.88-0.1405-0.46810.81490.01870.21480.3998-0.03940.728160.421991.700772.791
81.3667-0.2653-1.19790.81711.12012.81480.2686-0.1869-0.0347-0.04420.5308-0.1943-0.1060.2942-0.71210.39490.0893-0.05950.53970.07811.050966.968767.015567.5215
91.5464-0.646-0.47942.26241.23522.25560.1852-0.17220.177-0.3873-0.02030.3517-0.3501-0.1505-0.22280.449-0.0021-0.03010.5685-0.00490.518657.838770.342661.2574
100.1649-0.1205-0.40080.76170.73071.6552-0.00020.04450.03610.0083-0.00370.05970.0943-0.00520.00660.29090.0196-0.00820.37580.03640.318362.171359.925255.2355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 120 )A1 - 120
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 300 )A121 - 300
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 454 )A301 - 454
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 91 )B3 - 91
5X-RAY DIFFRACTION5chain 'B' and (resid 92 through 254 )B92 - 254
6X-RAY DIFFRACTION6chain 'B' and (resid 255 through 384 )B255 - 384
7X-RAY DIFFRACTION7chain 'B' and (resid 385 through 451 )B385 - 451
8X-RAY DIFFRACTION8chain 'C'C1 - 13
9X-RAY DIFFRACTION9chain 'D'D1 - 19
10X-RAY DIFFRACTION10chain 'S'S1 - 219

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