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- PDB-5o5y: Crystal structure of Thermococcus litoralis ADP-dependent glucoki... -

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Basic information

Entry
Database: PDB / ID: 5o5y
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
alpha-D-glucopyranose / TRIETHYLENE GLYCOL / ADP-dependent glucose/glucosamine kinase
Similarity search - Component
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.915 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

Downloads & links

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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)106,63514
Polymers105,3842
Non-polymers1,25112
Water12,701705
1
A: ADP-dependent glucokinase,ADP-dependent glucokinase,ADP-dependent glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4879
Polymers52,6921
Non-polymers7958
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)53,1485
Polymers52,6921
Non-polymers4564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.640, 97.610, 113.690
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 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-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
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 20% (w/v) PEG 3350, 30 mM glucose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 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: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.915→49.122 Å / Num. obs: 82817 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 37.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.0827 / Net I/σ(I): 15.81
Reflection shellResolution: 1.915→1.983 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 7810 / CC1/2: 0.905 / Rrim(I) all: 0.792 / % possible all: 95

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASER2.5phasing
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O5X

5o5x


Resolution: 1.915→49.122 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 4139 5 %
Rwork0.1708 --
obs0.1727 82790 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.915→49.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7226 0 82 705 8013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077489
X-RAY DIFFRACTIONf_angle_d0.83410111
X-RAY DIFFRACTIONf_dihedral_angle_d16.3144516
X-RAY DIFFRACTIONf_chiral_restr0.0521114
X-RAY DIFFRACTIONf_plane_restr0.0051311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.915-1.93670.32211160.27212205X-RAY DIFFRACTION85
1.9367-1.95950.3131360.24022592X-RAY DIFFRACTION100
1.9595-1.98340.27131380.232612X-RAY DIFFRACTION100
1.9834-2.00850.27071350.20882573X-RAY DIFFRACTION100
2.0085-2.03490.24641380.21132621X-RAY DIFFRACTION100
2.0349-2.06280.29921370.20752598X-RAY DIFFRACTION100
2.0628-2.09230.26031380.19362616X-RAY DIFFRACTION100
2.0923-2.12350.26721380.19342616X-RAY DIFFRACTION100
2.1235-2.15670.22911360.18742595X-RAY DIFFRACTION100
2.1567-2.19210.23411380.18942623X-RAY DIFFRACTION100
2.1921-2.22990.24951380.19092625X-RAY DIFFRACTION100
2.2299-2.27040.26621370.18662611X-RAY DIFFRACTION100
2.2704-2.31410.24721380.18472612X-RAY DIFFRACTION100
2.3141-2.36130.23471380.18812621X-RAY DIFFRACTION100
2.3613-2.41270.25021380.18852623X-RAY DIFFRACTION100
2.4127-2.46880.24761370.18082610X-RAY DIFFRACTION100
2.4688-2.53050.23281380.18542628X-RAY DIFFRACTION100
2.5305-2.59890.21121380.17782614X-RAY DIFFRACTION100
2.5989-2.67540.21321380.17752626X-RAY DIFFRACTION100
2.6754-2.76180.23971390.1762646X-RAY DIFFRACTION100
2.7618-2.86050.22461390.17722629X-RAY DIFFRACTION100
2.8605-2.9750.21861380.18182626X-RAY DIFFRACTION100
2.975-3.11030.21781390.18022644X-RAY DIFFRACTION100
3.1103-3.27430.22181400.17712650X-RAY DIFFRACTION100
3.2743-3.47940.23521390.16662654X-RAY DIFFRACTION100
3.4794-3.74790.17821400.15472662X-RAY DIFFRACTION100
3.7479-4.12490.16421410.14552675X-RAY DIFFRACTION100
4.1249-4.72140.16331410.13122686X-RAY DIFFRACTION100
4.7214-5.94690.15551440.15572728X-RAY DIFFRACTION100
5.9469-49.13830.17761490.16112830X-RAY DIFFRACTION99

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