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- PDB-5o0i: ADP-dependent glucokinase from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 5o0i
TitleADP-dependent glucokinase from Pyrococcus horikoshii
ComponentsADP-dependent 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
ACETATE ION / ADP-dependent glucose/glucosamine kinase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 2.0Jun 27, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _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 2.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: ADP-dependent glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,67611
Polymers51,8211
Non-polymers85610
Water3,063170
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-93 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.135, 77.135, 133.889
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-738-

HOH

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Components

#1: Protein ADP-dependent glucokinase / ADPGK


Mass: 51820.762 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)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: glkA, PH0589 / Production host: Escherichia coli (E. coli)
References: UniProt: O58328, ADP-specific glucose/glucosamine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG 6000, 0.2 M LiSO4, and 0.1 M citrate buffer (pH 3.6)

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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: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→47.3 Å / Num. obs: 31825 / % possible obs: 99.9 % / Redundancy: 19.78 % / CC1/2: 0.997 / Rrim(I) all: 0.264 / Net I/σ(I): 13.44
Reflection shellResolution: 2→2.072 Å / Redundancy: 20 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.556 / Rrim(I) all: 1.835 / % possible all: 99.2

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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: 2→44.63 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.52
RfactorNum. reflection% reflection
Rfree0.2191 1567 4.92 %
Rwork0.1684 --
obs0.1709 31825 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.84 Å2 / Biso mean: 37.9747 Å2 / Biso min: 11.75 Å2
Refinement stepCycle: final / Resolution: 2→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 62 170 3780
Biso mean--81.22 37.86 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123670
X-RAY DIFFRACTIONf_angle_d1.1464964
X-RAY DIFFRACTIONf_chiral_restr0.062559
X-RAY DIFFRACTIONf_plane_restr0.008627
X-RAY DIFFRACTIONf_dihedral_angle_d20.6982200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0001-2.06470.29491220.245927192841
2.0647-2.13850.30721460.216226932839
2.1385-2.22410.23521600.201626852845
2.2241-2.32530.25531330.183727262859
2.3253-2.44790.22291310.164127252856
2.4479-2.60120.26071320.168127422874
2.6012-2.8020.21711450.154327332878
2.802-3.0840.17351290.157327792908
3.084-3.53010.18881740.142827242898
3.5301-4.44690.18771350.140128102945
4.4469-44.64080.22631600.185529223082
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)
10.9408-0.1189-0.85512.10140.49130.6206-0.0595-0.1202-0.1076-0.05620.0692-0.08830.00790.0419-0.06820.15520.0049-0.08080.19380.02860.090238.1412-25.4333-20.6371
23.5211-0.0108-0.20223.6285-0.06233.03570.05330.00190.1064-0.15120.16160.81-0.1646-0.4961-0.02120.16180.0318-0.03760.26920.0850.329714.1979-1.0289-12.5535
31.9813-1.3347-0.83921.60010.19321.81320.0049-0.39310.1470.16540.0798-0.21710.02120.2826-0.08420.1849-0.0148-0.03280.2395-0.04340.144943.3857-11.1801-13.2094
44.2924-0.3747-0.96652.55260.35412.35460.2592-0.0989-0.2611-0.06470.1160.37010.1225-0.2401-0.05640.2179-0.0236-0.06480.17990.0710.249922.0567-7.916-13.5616
52.6783-1.0915-1.08074.13470.99542.27770.2339-0.02080.4504-0.0178-0.0215-0.4988-0.17760.3216-0.25460.1699-0.02640.03340.1614-0.01790.177849.0262-5.0077-24.9596
63.2645-0.03920.0681.58850.49291.047-0.05650.27890.2416-0.25170.05530.1097-0.2747-0.1127-0.11550.23850.03170.00490.19540.03960.147735.4924-8.3603-34.7605
73.07570.12590.91114.3705-1.14714.9039-0.10530.32130.0801-0.25250.11430.3495-0.2045-0.3453-0.00670.19480.0028-0.01250.2334-0.02220.126229.1727-23.3457-39.644
82.76621.40210.83372.6902-0.02433.460.1297-0.21880.0040.1185-0.10080.00620.2295-0.2291-0.01090.13290.01260.01990.16570.01230.144133.477-31.5036-28.3375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 43 )A4 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 106 )A44 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 169 )A107 - 169
4X-RAY DIFFRACTION4chain 'A' and (resid 170 through 211 )A170 - 211
5X-RAY DIFFRACTION5chain 'A' and (resid 212 through 234 )A212 - 234
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 305 )A235 - 305
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 359 )A306 - 359
8X-RAY DIFFRACTION8chain 'A' and (resid 360 through 457 )A360 - 457

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