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- PDB-5u0j: C-terminal ankyrin repeats from human kidney-type glutaminase (KG... -

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Basic information

Entry
Database: PDB / ID: 5u0j
TitleC-terminal ankyrin repeats from human kidney-type glutaminase (KGA) - monoclinic crystal form
ComponentsGlutaminase kidney isoform, mitochondrial
KeywordsHYDROLASE / Glutaminase / ankyrin / human / GLS1
Function / homology
Function and homology information


glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / mitochondrion / cytosol
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 / Beta-lactamase/transpeptidase-like / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsPasquali, C.C. / Gonzalez, A. / Dias, S.M.G. / Ambrosio, A.L.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/20673-2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaminase kidney isoform, mitochondrial
B: Glutaminase kidney isoform, mitochondrial
C: Glutaminase kidney isoform, mitochondrial
D: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,37310
Polymers63,2354
Non-polymers1386
Water11,458636
1
A: Glutaminase kidney isoform, mitochondrial
B: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6865
Polymers31,6172
Non-polymers693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-15 kcal/mol
Surface area8440 Å2
MethodPISA
2
C: Glutaminase kidney isoform, mitochondrial
D: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6865
Polymers31,6172
Non-polymers693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-16 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.490, 47.180, 115.698
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15808.714 Da / Num. of mol.: 4 / Fragment: UNP residues 551-669
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: O94925, glutaminase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.8 M NH4Cl, 0.1 M Bis-TRIS Propane

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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: 1.72→115.7 Å / Num. obs: 82659 / % possible obs: 94.1 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.72-1.756.30.7543030.902192.1
9.1-63.856.90.0241199.1

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Processing

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

5u0i


Resolution: 1.72→46.104 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 8391 5.21 %RANDOM
Rwork0.1835 ---
obs0.1854 160961 93.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→46.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 6 640 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193021
X-RAY DIFFRACTIONf_angle_d1.4544101
X-RAY DIFFRACTIONf_dihedral_angle_d2.3432461
X-RAY DIFFRACTIONf_chiral_restr0.089444
X-RAY DIFFRACTIONf_plane_restr0.011538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.73960.41552280.36144974X-RAY DIFFRACTION89
1.7396-1.760.3333110.32865169X-RAY DIFFRACTION96
1.76-1.78150.32433070.31835039X-RAY DIFFRACTION94
1.7815-1.8040.31132910.3235205X-RAY DIFFRACTION95
1.804-1.82780.33792830.29345172X-RAY DIFFRACTION95
1.8278-1.85280.34082880.28565085X-RAY DIFFRACTION95
1.8528-1.87930.34072900.28035220X-RAY DIFFRACTION95
1.8793-1.90730.32322650.31045116X-RAY DIFFRACTION94
1.9073-1.93710.42582530.34655150X-RAY DIFFRACTION95
1.9371-1.96890.25582800.23585168X-RAY DIFFRACTION94
1.9689-2.00280.29932980.21855066X-RAY DIFFRACTION95
2.0028-2.03930.2512650.2234655X-RAY DIFFRACTION85
2.0393-2.07850.2682620.21064507X-RAY DIFFRACTION84
2.0785-2.12090.2032830.18965232X-RAY DIFFRACTION95
2.1209-2.1670.21193290.18545118X-RAY DIFFRACTION96
2.167-2.21740.20562180.18165190X-RAY DIFFRACTION95
2.2174-2.27290.33423010.25665075X-RAY DIFFRACTION93
2.2729-2.33430.21793300.18245145X-RAY DIFFRACTION96
2.3343-2.4030.24012720.17885295X-RAY DIFFRACTION96
2.403-2.48060.20642950.16425246X-RAY DIFFRACTION96
2.4806-2.56920.18752460.16515199X-RAY DIFFRACTION95
2.5692-2.67210.2182260.16374367X-RAY DIFFRACTION81
2.6721-2.79370.20592980.17855299X-RAY DIFFRACTION98
2.7937-2.9410.26243450.19025326X-RAY DIFFRACTION98
2.941-3.12520.21853210.18715206X-RAY DIFFRACTION97
3.1252-3.36640.21242080.18515343X-RAY DIFFRACTION97
3.3664-3.70510.16372350.14185057X-RAY DIFFRACTION93
3.7051-4.24090.14942420.12754841X-RAY DIFFRACTION88
4.2409-5.34180.19123220.13455233X-RAY DIFFRACTION97
5.3418-46.1210.18312990.16064872X-RAY DIFFRACTION90

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