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- PDB-5o0j: ADP-dependent glucokinase from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 5o0j
TitleADP-dependent glucokinase from Pyrococcus horikoshii
ComponentsADP-dependent glucokinaseADP-specific glucokinase
KeywordsTRANSFERASE / ADP-dependent glucokinase
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 / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...ADP-dependent glucose/glucosamine kinase, archaeal / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
8-BROMO-ADENOSINE-5'-MONOPHOSPHATE / alpha-D-glucopyranose / ADP-dependent glucose/glucosamine kinase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsGrudnik, P. / Dubin, G.
Funding support Poland, 2items
OrganizationGrant numberCountry
National Science CenterUMO-2015/19/D/NZ1/02009 Poland
National Science CenterUMO-2012/07/E/NZ1/01907 Poland
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for ADP-dependent glucokinase inhibition by 8-bromo-substituted adenosine nucleotide.
Authors: Grudnik, P. / Kaminski, M.M. / Rembacz, K.P. / Kuska, K. / Madej, M. / Potempa, J. / Dawidowski, M. / Dubin, G.
History
DepositionMay 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 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 1.4Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7224
Polymers51,6901
Non-polymers1,0323
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-2 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.838, 74.714, 62.951
Angle α, β, γ (deg.)90.000, 99.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 51689.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Gene: glkA, PH0589 / Production host: Escherichia coli (E. coli)
References: UniProt: O58328, ADP-specific glucose/glucosamine kinase
#2: Chemical ChemComp-8BR / 8-BROMO-ADENOSINE-5'-MONOPHOSPHATE


Mass: 426.117 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13BrN5O7P
#3: 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
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: ammonium nitrate (0.2 M) and polyethylene glycol 3350 (20%)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.81→46.19 Å / Num. obs: 46884 / % possible obs: 97.1 % / Redundancy: 3.39 % / CC1/2: 0.996 / Rrim(I) all: 0.109 / Net I/σ(I): 9.17
Reflection shellResolution: 1.81→1.875 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.81 / CC1/2: 0.732 / Rrim(I) all: 0.694 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1l2l

1l2l


Resolution: 1.81→45.977 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 2099 4.48 %
Rwork0.1608 44780 -
obs0.1626 46879 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.75 Å2 / Biso mean: 28.8763 Å2 / Biso min: 10.15 Å2
Refinement stepCycle: final / Resolution: 1.81→45.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 60 522 4228
Biso mean--24.54 38.48 -
Num. residues----453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073793
X-RAY DIFFRACTIONf_angle_d0.9575128
X-RAY DIFFRACTIONf_chiral_restr0.069575
X-RAY DIFFRACTIONf_plane_restr0.006673
X-RAY DIFFRACTIONf_dihedral_angle_d15.7472313
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 (%)
1.8102-1.85230.29591130.26822420253380
1.8523-1.89870.2941400.25792984312498
1.8987-1.950.32561410.25723016315798
1.95-2.00740.24961410.22422992313398
2.0074-2.07220.23721420.19013026316898
2.0722-2.14620.22191380.18232960309898
2.1462-2.23220.21441410.17873002314397
2.2322-2.33370.23871430.17563038318199
2.3337-2.45680.18191420.15093031317399
2.4568-2.61070.20041430.15593061320499
2.6107-2.81220.18971400.15612973311397
2.8122-3.09520.18851430.14983061320499
3.0952-3.54290.17861440.14393070321499
3.5429-4.46310.16881430.13043035317898
4.4631-45.99210.18771450.13993111325699
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)
11.46160.2026-0.22410.68640.06141.0784-0.0113-0.1182-0.12580.01510.0043-0.1940.08760.1063-0.02980.158-0.00240.02280.09660.01570.246931.892731.513224.2899
22.8511-0.18050.49490.7615-0.35470.889-0.0153-0.1217-0.01650.0910.01130.0248-0.0199-0.00360.01530.18250.00330.01530.1247-0.0160.164621.31537.140728.7967
31.1597-0.7415-0.27611.70240.08781.5431-0.01140.0524-0.1367-0.0799-0.01950.1220.15370.02660.03640.1644-0.0238-0.00050.1407-0.00120.171416.422720.884917.7896
41.7753-0.1785-0.04611.8071-0.16541.58530.02710.24460.0189-0.2434-0.0227-0.1531-0.03630.1191-0.03170.15080.00790.04150.18160.02580.115126.999331.78014.9535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 86 )A5 - 86
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 215 )A87 - 215
3X-RAY DIFFRACTION3chain 'A' and (resid 216 through 337 )A216 - 337
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 457 )A338 - 457

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