[English] 日本語
Yorodumi
- PDB-5ccf: Structure of Mouse ADP-Dependent Glucokinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ccf
TitleStructure of Mouse ADP-Dependent Glucokinase
ComponentsADP-dependent glucokinase
KeywordsTRANSFERASE / ADPGK / glucose-6-phosphate / ribokinase / kinase
Function / homology
Function and homology information


ADP-specific glucose/glucosamine kinase / ADP-specific glucokinase activity / Glycolysis / glycolytic process / glucose metabolic process / extracellular region / metal ion binding
Similarity search - Function
ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Ribokinase-like
Similarity search - Domain/homology
ADP-dependent glucokinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRichter, J.P. / Ronimus, R.S. / Sutherland-Smith, A.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand Marsden GrantAGR0702 New Zealand
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Structural and Functional Characterization of Mammalian ADP-dependent Glucokinase.
Authors: Richter, J.P. / Goroncy, A.K. / Ronimus, R.S. / Sutherland-Smith, A.J.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-dependent glucokinase


Theoretical massNumber of molelcules
Total (without water)53,0681
Polymers53,0681
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.923, 58.686, 160.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ADP-dependent glucokinase / ADPGK


Mass: 53067.738 Da / Num. of mol.: 1 / Fragment: UNP residues 51-495
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adpgk / Plasmid: pBAD-TOPO / Production host: Escherichia coli (E. coli)
References: UniProt: Q8VDL4, ADP-specific glucose/glucosamine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NH4Cl, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2012
RadiationMonochromator: Double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.094→47.416 Å / Num. all: 26310 / Num. obs: 26310 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/av σ(I): 9.3 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1UA4, 1L2L, & 1GC5

1ua4

1l2l

1gc5


Resolution: 2.1→47.4 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.502 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24416 1318 5 %RANDOM
Rwork0.19299 ---
obs0.19557 24797 99.54 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.201 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---0.06 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 0 279 3718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193534
X-RAY DIFFRACTIONr_bond_other_d0.0020.023352
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9484807
X-RAY DIFFRACTIONr_angle_other_deg0.88137704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82823.913161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5215569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1061522
X-RAY DIFFRACTIONr_chiral_restr0.0730.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02826
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3015.4951787
X-RAY DIFFRACTIONr_mcbond_other2.2995.4921786
X-RAY DIFFRACTIONr_mcangle_it3.61312.332233
X-RAY DIFFRACTIONr_mcangle_other3.61212.3362234
X-RAY DIFFRACTIONr_scbond_it2.6426.0761747
X-RAY DIFFRACTIONr_scbond_other2.6416.0831748
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.17113.3652573
X-RAY DIFFRACTIONr_long_range_B_refined6.60916.1044069
X-RAY DIFFRACTIONr_long_range_B_other6.54115.8583960
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 98 -
Rwork0.293 1779 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 9.5655 Å / Origin y: -0.782 Å / Origin z: -20.6669 Å
111213212223313233
T0.1397 Å20.0333 Å2-0.0131 Å2-0.0178 Å2-0.003 Å2--0.1931 Å2
L0.1452 °20.1033 °20.1619 °2-0.385 °20.305 °2--0.4195 °2
S0.0418 Å °0.0267 Å °0.0573 Å °-0.082 Å °0.0356 Å °0.0124 Å °0.0595 Å °0.0686 Å °-0.0775 Å °

+
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