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- PDB-5o5z: CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS ADP-DEPENDENT GLUCOKI... -

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Basic information

Entry
Database: PDB / ID: 5o5z
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
Chem-AT4 / alpha-D-glucopyranose / ADP-dependent glucose/glucosamine kinase
Similarity search - Component
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.441 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: 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

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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)107,46816
Polymers105,3842
Non-polymers2,08414
Water1,27971
1
A: ADP-dependent glucokinase,ADP-dependent glucokinase,ADP-dependent glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7849
Polymers52,6921
Non-polymers1,0928
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)53,6847
Polymers52,6921
Non-polymers9926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.282, 97.835, 113.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#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 (archaea) / Gene: glkA, OCC_09701 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7M537, ADP-specific glucose/glucosamine kinase
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 84 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AT4 / 5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE / ADENOSINE 5'-O-(2-THIODIPHOSPHATE)


Mass: 443.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O9P2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 20% (w/v) PEG 3350, 30 mM glucose, 5 mM Mg2+-ADPbetaS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.8233 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / 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: 1.8233 Å / Relative weight: 1
ReflectionResolution: 2.441→58.729 Å / Num. obs: 40470 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 49.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0765 / Rrim(I) all: 0.0836 / Net I/σ(I): 14.56
Reflection shellResolution: 2.441→2.529 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.74 / Num. unique obs: 3972 / CC1/2: 0.89 / Rsym value: 0.807 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wwPDB 4B8R

4b8r


Resolution: 2.441→58.729 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 2033 5.02 %RANDOM
Rwork0.1949 ---
obs0.1963 40460 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.441→58.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7226 0 131 71 7428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037489
X-RAY DIFFRACTIONf_angle_d0.61210118
X-RAY DIFFRACTIONf_dihedral_angle_d15.4724493
X-RAY DIFFRACTIONf_chiral_restr0.0451115
X-RAY DIFFRACTIONf_plane_restr0.0031299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4414-2.49820.34221270.30962523X-RAY DIFFRACTION100
2.4982-2.56070.30161290.28282513X-RAY DIFFRACTION100
2.5607-2.62990.31031470.26452532X-RAY DIFFRACTION100
2.6299-2.70730.25931370.23692520X-RAY DIFFRACTION100
2.7073-2.79470.27571240.24312547X-RAY DIFFRACTION100
2.7947-2.89450.23551130.22612535X-RAY DIFFRACTION100
2.8945-3.01040.28931410.23332555X-RAY DIFFRACTION100
3.0104-3.14740.30331220.24732551X-RAY DIFFRACTION100
3.1474-3.31340.26291450.22142541X-RAY DIFFRACTION100
3.3134-3.52090.25681220.20172559X-RAY DIFFRACTION100
3.5209-3.79270.21731330.1852580X-RAY DIFFRACTION100
3.7927-4.17430.16391180.1672583X-RAY DIFFRACTION100
4.1743-4.77810.1781610.14982556X-RAY DIFFRACTION100
4.7781-6.0190.20341550.17322619X-RAY DIFFRACTION100
6.019-58.74640.1951590.17442713X-RAY DIFFRACTION100
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)
13.1949-1.43690.49592.19480.1392.2083-0.1452-0.05380.04130.30840.1348-0.20660.03030.42140.0350.3727-0.0632-0.0090.42120.06080.3021117.0487101.7273109.205
22.27-0.79420.232.255-0.66342.71010.10980.2859-0.0152-0.1193-0.089-0.09750.08020.1735-0.02020.28590.0410.01490.3574-0.01380.3112114.054199.710693.7563
34.96361.5919-1.90444.7182-0.36036.41-0.01450.16480.3033-0.23730.02070.0885-0.4546-0.36330.04590.32630.1039-0.03740.36560.03020.3428103.9501118.828102.0044
41.57770.01480.54881.7961-1.22213.2203-0.0646-0.08390.34340.16580.0357-0.2769-0.67010.30090.08120.5920.06380.02620.4092-0.15490.7097114.303134.9339143.2002
53.4828-0.80691.55021.7707-0.06263.156-0.2073-0.55520.24070.19580.14330.1566-0.3549-0.55620.05510.5060.12570.04990.4419-0.03860.477103.7168127.5221151.4171
62.6713-0.6370.58781.9784-0.53392.23670.0009-0.22450.1862-0.01390.03620.1045-0.1373-0.0958-0.03450.39230.09060.05480.5021-0.03770.4155107.6413120.994145.4883
73.20730.83-1.17222.5438-1.83114.31840.0228-0.23270.10130.02190.0341-0.0907-0.11980.2620.00080.30610.0228-0.0180.3001-0.06210.3318113.2568121.7781129.4055
84.17991.7335-1.59414.14380.46198.22240.34-0.05950.5807-0.3901-0.03690.1179-1.2573-0.1631-0.2790.66390.06310.00550.30920.0310.6503109.439139.9492129.9902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 111 )
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 298 )
3X-RAY DIFFRACTION3chain 'A' and (resid 299 through 454 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 77 )
5X-RAY DIFFRACTION5chain 'B' and (resid 78 through 189 )
6X-RAY DIFFRACTION6chain 'B' and (resid 190 through 254 )
7X-RAY DIFFRACTION7chain 'B' and (resid 255 through 384 )
8X-RAY DIFFRACTION8chain 'B' and (resid 385 through 451 )

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