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- PDB-8gwr: Near full length Kidney type Glutaminase in complex with 2,2-Dime... -

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Basic information

Entry
Database: PDB / ID: 8gwr
TitleNear full length Kidney type Glutaminase in complex with 2,2-Dimethyl-2,3-Dihydrobenzo[a] Phenanthridin-4(1H)-one (DDP)
ComponentsGlutaminase kidney isoform, mitochondrial
KeywordsONCOPROTEIN / Glutaminase / complex / allosteric inhibition / small molecule inhibitor / cancer
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 repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Beta-lactamase/transpeptidase-like / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-HZO / Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsShankar, S. / Jobichen, C. / Sivaraman, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)R154-000-A72-114 Singapore
CitationJournal: Febs J. / Year: 2023
Title: A novel allosteric site employs a conserved inhibition mechanism in human kidney-type glutaminase.
Authors: Shankar, S. / Ramachandran, S. / Tulsian, N. / Radhakrishnan, S. / Jobichen, C. / Sivaraman, J.
History
DepositionSep 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,3833
Polymers147,1082
Non-polymers2751
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-26 kcal/mol
Surface area37060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.194, 143.194, 167.488
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 73553.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O94925, glutaminase
#2: Chemical ChemComp-HZO / 2,2-dimethyl-1,3-dihydrobenzo[a]phenanthridin-4-one


Mass: 275.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.5M sodium malonate pH 7, 4% jeffamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 94454 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 31.47
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 3870 / Rsym value: 0.718

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOY

3voy


Resolution: 2.801→46.871 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2362 3870 4.1 %
Rwork0.2042 --
obs0.2055 94454 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.801→46.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7633 0 21 46 7700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.801-2.83510.32891380.30713213X-RAY DIFFRACTION100
2.8351-2.8710.27241400.27533278X-RAY DIFFRACTION100
2.871-2.90880.27611400.2643177X-RAY DIFFRACTION100
2.9088-2.94860.35941360.27623225X-RAY DIFFRACTION100
2.9486-2.99070.32261480.29173298X-RAY DIFFRACTION100
2.9907-3.03540.35651360.28273187X-RAY DIFFRACTION100
3.0354-3.08280.26571340.26613202X-RAY DIFFRACTION100
3.0828-3.13330.29041320.25383308X-RAY DIFFRACTION100
3.1333-3.18730.27641340.25113263X-RAY DIFFRACTION100
3.1873-3.24530.28931400.24933224X-RAY DIFFRACTION100
3.2453-3.30770.25021400.24123222X-RAY DIFFRACTION100
3.3077-3.37520.28221400.22833199X-RAY DIFFRACTION100
3.3752-3.44860.2781400.2233249X-RAY DIFFRACTION100
3.4486-3.52870.2911460.23513215X-RAY DIFFRACTION100
3.5287-3.6170.27891340.21963263X-RAY DIFFRACTION100
3.617-3.71470.24541320.21093225X-RAY DIFFRACTION100
3.7147-3.8240.26551400.19513238X-RAY DIFFRACTION100
3.824-3.94730.24581360.1963265X-RAY DIFFRACTION100
3.9473-4.08830.23871400.18143252X-RAY DIFFRACTION100
4.0883-4.25190.19651380.17753201X-RAY DIFFRACTION100
4.2519-4.44530.21421460.1653221X-RAY DIFFRACTION100
4.4453-4.67950.19481340.16043270X-RAY DIFFRACTION100
4.6795-4.97240.17291340.16763227X-RAY DIFFRACTION100
4.9724-5.35580.19981320.17623232X-RAY DIFFRACTION100
5.3558-5.89380.27911440.20593237X-RAY DIFFRACTION100
5.8938-6.74450.22821440.22013224X-RAY DIFFRACTION100
6.7445-8.48910.15471340.17893258X-RAY DIFFRACTION100
8.4891-46.7090.17621380.16463211X-RAY DIFFRACTION99

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