[English] 日本語
Yorodumi
- PDB-5u0k: C-terminal ankyrin repeats from human liver-type glutaminase (GAB/LGA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u0k
TitleC-terminal ankyrin repeats from human liver-type glutaminase (GAB/LGA)
ComponentsGlutaminase liver isoform, mitochondrial
KeywordsHYDROLASE / Glutaminase / ankyrin / human / GLS2
Function / homology
Function and homology information


L-glutamine catabolic process / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutaminase / Glutamate Neurotransmitter Release Cycle / glutaminase activity / amino acid metabolic process / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / regulation of apoptotic process ...L-glutamine catabolic process / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutaminase / Glutamate Neurotransmitter Release Cycle / glutaminase activity / amino acid metabolic process / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / regulation of apoptotic process / mitochondrial matrix / mitochondrion
Similarity search - Function
Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Beta-lactamase/transpeptidase-like / ankyrin repeats ...Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Beta-lactamase/transpeptidase-like / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Glutaminase liver isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.548 Å
AuthorsFerreira, I.M. / Pasquali, C.C. / Gonzalez, A. / Dias, S.M.G. / Ambrosio, A.L.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)201/20673-2 Brazil
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats.
Authors: Pasquali, C.C. / Islam, Z. / Adamoski, D. / Ferreira, I.M. / Righeto, R.D. / Bettini, J. / Portugal, R.V. / Yue, W.W. / Gonzalez, A. / Dias, S.M.G. / Ambrosio, A.L.B.
History
DepositionNov 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references / Structure summary
Revision 1.2Feb 6, 2019Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaminase liver isoform, mitochondrial
B: Glutaminase liver isoform, mitochondrial
C: Glutaminase liver isoform, mitochondrial
D: Glutaminase liver isoform, mitochondrial
E: Glutaminase liver isoform, mitochondrial
F: Glutaminase liver isoform, mitochondrial
G: Glutaminase liver isoform, mitochondrial
H: Glutaminase liver isoform, mitochondrial
I: Glutaminase liver isoform, mitochondrial
J: Glutaminase liver isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)158,40710
Polymers158,40710
Non-polymers00
Water2,126118
1
A: Glutaminase liver isoform, mitochondrial
F: Glutaminase liver isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)31,6812
Polymers31,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaminase liver isoform, mitochondrial
C: Glutaminase liver isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)31,6812
Polymers31,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Glutaminase liver isoform, mitochondrial
E: Glutaminase liver isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)31,6812
Polymers31,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Glutaminase liver isoform, mitochondrial
I: Glutaminase liver isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)31,6812
Polymers31,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: Glutaminase liver isoform, mitochondrial
J: Glutaminase liver isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)31,6812
Polymers31,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.260, 85.260, 336.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
Glutaminase liver isoform, mitochondrial / GLS / L-glutaminase / L-glutamine amidohydrolase


Mass: 15840.733 Da / Num. of mol.: 10 / Fragment: UNP residues 485-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLS2, GA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q9UI32, glutaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.1 M tri-sodium citrate, 0.1 M imidazole, 20 mM glutamine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2015 / Details: Rh coated mirror
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→84.2 Å / Num. obs: 45005 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.55-2.648.10.67744130.86199.8
9.87-84.28.50.0450.999198.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
Aimless0.5.28data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U0I

5u0i


Resolution: 2.548→38.033 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 4677 5.25 %RANDOM
Rwork0.2181 ---
obs0.2202 89114 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.548→38.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7607 0 0 118 7725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027757
X-RAY DIFFRACTIONf_angle_d0.44910509
X-RAY DIFFRACTIONf_dihedral_angle_d2.1234635
X-RAY DIFFRACTIONf_chiral_restr0.0371184
X-RAY DIFFRACTIONf_plane_restr0.0031358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5481-2.57710.33371280.28532872X-RAY DIFFRACTION100
2.5771-2.60740.35011680.28792798X-RAY DIFFRACTION100
2.6074-2.63920.35451440.28742814X-RAY DIFFRACTION100
2.6392-2.67260.32131640.29932841X-RAY DIFFRACTION100
2.6726-2.70770.37881620.30562751X-RAY DIFFRACTION100
2.7077-2.74480.3951840.29872891X-RAY DIFFRACTION100
2.7448-2.7840.35241920.29642738X-RAY DIFFRACTION100
2.784-2.82560.3621240.30582881X-RAY DIFFRACTION100
2.8256-2.86970.39251650.28872753X-RAY DIFFRACTION99
2.8697-2.91670.35531350.29262841X-RAY DIFFRACTION99
2.9167-2.9670.41541620.28982780X-RAY DIFFRACTION100
2.967-3.02090.34791040.28562889X-RAY DIFFRACTION100
3.0209-3.0790.35431640.26772828X-RAY DIFFRACTION100
3.079-3.14180.34311690.26422814X-RAY DIFFRACTION100
3.1418-3.21010.29971840.25572720X-RAY DIFFRACTION100
3.2101-3.28480.27891320.23732912X-RAY DIFFRACTION100
3.2848-3.36690.28641260.23122820X-RAY DIFFRACTION99
3.3669-3.45780.27271760.21872772X-RAY DIFFRACTION100
3.4578-3.55950.2671630.23182811X-RAY DIFFRACTION99
3.5595-3.67430.25121240.20372829X-RAY DIFFRACTION100
3.6743-3.80550.22961660.18952764X-RAY DIFFRACTION99
3.8055-3.95770.22731680.18992825X-RAY DIFFRACTION100
3.9577-4.13760.23081940.17992770X-RAY DIFFRACTION100
4.1376-4.35550.22211690.17852830X-RAY DIFFRACTION100
4.3555-4.62790.2531660.18322783X-RAY DIFFRACTION99
4.6279-4.98450.22681730.17622805X-RAY DIFFRACTION99
4.9845-5.48480.15071290.17632869X-RAY DIFFRACTION100
5.4848-6.27540.18341680.18882787X-RAY DIFFRACTION100
6.2754-7.89480.23931350.19222830X-RAY DIFFRACTION99
7.8948-38.03690.17751390.20062819X-RAY DIFFRACTION99

+
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