[English] 日本語
Yorodumi
- PDB-5o5x: Crystal structure of Thermococcus litoralis ADP-dependent glucoki... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more