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- PDB-4o7d: Crystal structure of human glutaminase in complex DON -

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Basic information

Entry
Database: PDB / ID: 4o7d
TitleCrystal structure of human glutaminase in complex DON
ComponentsGlutaminase kidney isoform, mitochondrial
KeywordsHYDROLASE
Function / homology
Function and homology information


L-glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutaminase / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...L-glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutaminase / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / protein homotetramerization / chemical synaptic transmission / mitochondrial matrix / synapse / mitochondrion / cytosol
Similarity search - Function
Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats ...Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Beta-lactamase/transpeptidase-like / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-OXO-L-NORLEUCINE / Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThangavelu, K. / Sivaraman, J.
CitationJournal: Sci Rep / Year: 2014
Title: Structural basis for the active site inhibition mechanism of human kidney-type glutaminase (KGA)
Authors: Thangavelu, K. / Chong, Q.Y. / Low, B.C. / Sivaraman, J.
History
DepositionDec 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6072
Polymers34,4611
Non-polymers1451
Water1,54986
1
A: Glutaminase kidney isoform, mitochondrial
hetero molecules

A: Glutaminase kidney isoform, mitochondrial
hetero molecules

A: Glutaminase kidney isoform, mitochondrial
hetero molecules

A: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,4268
Polymers137,8454
Non-polymers5814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_556y,x,-z+11
Buried area6630 Å2
ΔGint-38 kcal/mol
Surface area43310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.278, 139.278, 155.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-751-

HOH

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Components

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


Mass: 34461.355 Da / Num. of mol.: 1 / Fragment: UNP Residues 221-531
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, glutaminase
#2: Chemical ChemComp-ONL / 5-OXO-L-NORLEUCINE


Type: L-peptide linking / Mass: 145.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.470732 Å3/Da / Density % sol: 77.516716 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M Bis-Tris propane (pH 7.2), 1.8M Lithium Sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 34102 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.771 Å / FOM work R set: 0.8508 / SU ML: 0.61 / σ(F): 1.42 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 1722 5.06 %
Rwork0.1928 --
obs0.1937 34035 99.59 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.353 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 150.74 Å2 / Biso mean: 54.57 Å2 / Biso min: 29.59 Å2
Baniso -1Baniso -2Baniso -3
1--9.3778 Å2-0 Å20 Å2
2---9.3778 Å2-0 Å2
3---18.7556 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 10 86 2508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072481
X-RAY DIFFRACTIONf_angle_d1.023353
X-RAY DIFFRACTIONf_dihedral_angle_d14.868897
X-RAY DIFFRACTIONf_chiral_restr0.07361
X-RAY DIFFRACTIONf_plane_restr0.005438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.36770.31821400.29092584272496
2.3677-2.44410.28161420.26232624276699
2.4441-2.53130.26421250.252226932818100
2.5313-2.63260.28841440.221126572801100
2.6326-2.75230.23861420.223126822824100
2.7523-2.89720.23831510.208526612812100
2.8972-3.07850.23121240.204727132837100
3.0785-3.31570.22191490.197126802829100
3.3157-3.64850.20851530.191926902843100
3.6485-4.17460.17681540.163827072861100
4.1746-5.25220.17551590.154627392898100
5.2522-25.77220.20481390.196128833022100

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