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- PDB-7rgg: Room temperature serial crystal structure of Glutaminase C in com... -

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Basic information

Entry
Database: PDB / ID: 7rgg
TitleRoom temperature serial crystal structure of Glutaminase C in complex with inhibitor BPTES
ComponentsGlutaminase kidney isoform, mitochondrial 68 kDa chain
KeywordsHYDROLASE/INHIBITOR / Inhibitor / Complex / HYDROLASE-INHIBITOR complex
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-04A / Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMilano, S.K. / Finke, A. / Cerione, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: New insights into the molecular mechanisms of glutaminase C inhibitors in cancer cells using serial room temperature crystallography.
Authors: Milano, S.K. / Huang, Q. / Nguyen, T.T. / Ramachandran, S. / Finke, A. / Kriksunov, I. / Schuller, D.J. / Szebenyi, D.M. / Arenholz, E. / McDermott, L.A. / Sukumar, N. / Cerione, R.A. / Katt, W.P.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Glutaminase kidney isoform, mitochondrial 68 kDa chain
B: Glutaminase kidney isoform, mitochondrial 68 kDa chain
C: Glutaminase kidney isoform, mitochondrial 68 kDa chain
D: Glutaminase kidney isoform, mitochondrial 68 kDa chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,9796
Polymers215,9304
Non-polymers1,0492
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-46 kcal/mol
Surface area60880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.000, 138.000, 178.000
Angle α, β, γ (deg.)90.000, 90.001, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Glutaminase kidney isoform, mitochondrial 68 kDa chain


Mass: 53982.512 Da / Num. of mol.: 4 / Fragment: UNP residues 72-550
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Production host: Escherichia coli (E. coli) / References: UniProt: O94925, Hydrolases
#2: Chemical ChemComp-04A / N,N'-[sulfanediylbis(ethane-2,1-diyl-1,3,4-thiadiazole-5,2-diyl)]bis(2-phenylacetamide) / BPTES


Mass: 524.681 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24N6O2S3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.0 M lithium chloride, 10% PEG6000, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: G3 / Wavelength: 1.127 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 3→20.33 Å / Num. obs: 47136 / % possible obs: 97.6 % / Redundancy: 19.8 % / Biso Wilson estimate: 79.49 Å2 / CC1/2: 0.97 / Net I/σ(I): 5.4
Reflection shellResolution: 3→3.07 Å / Num. unique obs: 4690 / Rpim(I) all: 0.45 / % possible all: 98.6
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WJ6

5wj6


Resolution: 3→20.33 Å / SU ML: 0.4361 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2861 2000 4.26 %
Rwork0.2074 44924 -
obs0.2108 46924 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.83 Å2
Refinement stepCycle: LAST / Resolution: 3→20.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12293 0 70 4 12367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009112636
X-RAY DIFFRACTIONf_angle_d1.189317074
X-RAY DIFFRACTIONf_chiral_restr0.05821878
X-RAY DIFFRACTIONf_plane_restr0.00762221
X-RAY DIFFRACTIONf_dihedral_angle_d23.02324549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.41921330.33483139X-RAY DIFFRACTION95.48
3.07-3.160.3781460.31613184X-RAY DIFFRACTION96.94
3.16-3.250.40781430.28463157X-RAY DIFFRACTION97.63
3.25-3.350.32571500.26083294X-RAY DIFFRACTION98.51
3.35-3.470.34441420.23533197X-RAY DIFFRACTION97.89
3.47-3.610.31991480.21783228X-RAY DIFFRACTION98.37
3.61-3.780.29011440.20093228X-RAY DIFFRACTION97.6
3.78-3.970.28151450.19573202X-RAY DIFFRACTION98.33
3.97-4.220.26371410.19083247X-RAY DIFFRACTION98.15
4.22-4.540.26691440.17823261X-RAY DIFFRACTION97.93
4.54-4.990.24661430.17993218X-RAY DIFFRACTION97.25
4.99-5.70.2511350.19953198X-RAY DIFFRACTION97.4
5.7-7.130.32981460.22893241X-RAY DIFFRACTION96.99
7.13-20.330.24331400.17393130X-RAY DIFFRACTION93.62
Refinement TLS params.Method: refined / Origin x: -4.18691489875 Å / Origin y: 33.9860666187 Å / Origin z: -44.690465283 Å
111213212223313233
T0.510982783713 Å20.00274456582206 Å20.0132516267596 Å2-0.502734139294 Å20.00655739224241 Å2--0.577983973288 Å2
L0.2037269325 °20.00805022076002 °20.0293786888587 °2-0.485352274985 °2-0.2257213526 °2--1.23506353144 °2
S-0.0297348541059 Å °0.00490467898344 Å °0.0165641875417 Å °-0.0389810303516 Å °0.0978061597412 Å °-0.00292077702401 Å °-0.031152344714 Å °0.0169059307401 Å °-0.0603960675773 Å °
Refinement TLS groupSelection details: all

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