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- PDB-5u0k: C-terminal ankyrin repeats from human liver-type glutaminase (GAB/LGA) -

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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


glutamine catabolic process / glutamate biosynthetic process / Glutamate and glutamine metabolism / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / amino acid metabolic process / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / regulation of apoptotic process ...glutamine catabolic process / glutamate biosynthetic process / Glutamate and glutamine metabolism / Glutamate Neurotransmitter Release Cycle / glutaminase / 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. / ankyrin repeats / Ankyrin repeat ...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. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Beta-lactamase/transpeptidase-like / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.23 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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