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- PDB-4bqm: Crystal structure of human liver-type glutaminase, catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4bqm
TitleCrystal structure of human liver-type glutaminase, catalytic domain
ComponentsGLUTAMINASE LIVER ISOFORM, MITOCHONDRIAL
KeywordsHYDROLASE
Function / homology
Function and homology information


L-glutamine catabolic process / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutaminase / Glutamate Neurotransmitter Release Cycle / glutaminase activity / amino acid metabolic process / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / regulation of apoptotic process ...L-glutamine catabolic process / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutaminase / Glutamate Neurotransmitter Release Cycle / 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 / 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 / Ankyrin repeat / Beta-lactamase/transpeptidase-like / Ankyrin repeat-containing domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaminase liver isoform, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsFerreira, I.M. / Vollmar, M. / Krojer, T. / Strain-Damerell, C. / Froese, S. / Coutandin, D. / Williams, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. ...Ferreira, I.M. / Vollmar, M. / Krojer, T. / Strain-Damerell, C. / Froese, S. / Coutandin, D. / Williams, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Dias, S.M.G. / Ambrosio, A.L.B. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of Human Liver-Type Glutaminase, Catalytic Domain
Authors: Ferreira, I.M. / Vollmar, M. / Krojer, T. / Strain-Damerell, C. / Froese, S. / Coutandin, D. / Williams, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. ...Authors: Ferreira, I.M. / Vollmar, M. / Krojer, T. / Strain-Damerell, C. / Froese, S. / Coutandin, D. / Williams, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Dias, S.M.G. / Ambrosio, A.L.B. / Yue, W.W.
History
DepositionMay 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: GLUTAMINASE LIVER ISOFORM, MITOCHONDRIAL
B: GLUTAMINASE LIVER ISOFORM, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3279
Polymers76,9462
Non-polymers3817
Water3,027168
1
A: GLUTAMINASE LIVER ISOFORM, MITOCHONDRIAL
B: GLUTAMINASE LIVER ISOFORM, MITOCHONDRIAL
hetero molecules

A: GLUTAMINASE LIVER ISOFORM, MITOCHONDRIAL
B: GLUTAMINASE LIVER ISOFORM, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,65518
Polymers153,8924
Non-polymers76214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area9500 Å2
ΔGint-57.4 kcal/mol
Surface area42670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.613, 203.613, 98.965
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2055-

HOH

21B-2011-

HOH

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Components

#1: Protein GLUTAMINASE LIVER ISOFORM, MITOCHONDRIAL / GLS / L-GLUTAMINASE / L-GLUTAMINE AMIDOHYDROLASE / HUMAN LIVER-TYPE GLUTAMINASE


Mass: 38473.039 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 154-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9UI32, glutaminase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLYFQSM AT START BELONG TO EXPRESSION TAG

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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: 2.57 Å3/Da / Density % sol: 52.22 % / Description: NONE
Crystal growDetails: 0.1M TRIS PH 8.5, 0.2M SODIUM CHLORIDE, 25%(W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.18→65.83 Å / Num. obs: 40642 / % possible obs: 100 % / Observed criterion σ(I): 4.4 / Redundancy: 11.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.5
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SS4

3ss4


Resolution: 2.18→65.92 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.364 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY DENSITY AT THE INTERFACE BETWEEN CHAIN A AND SYMMETRY MOLECULE OF CHAIN B AROUND RESIDUE LEU254 PROBABLY UNKNOWN LIGAND.
RfactorNum. reflection% reflectionSelection details
Rfree0.20324 2036 5 %RANDOM
Rwork0.17699 ---
obs0.17833 38604 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.816 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.11 Å2-0 Å2
2--0.11 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.18→65.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4568 0 22 168 4758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194690
X-RAY DIFFRACTIONr_bond_other_d0.0050.024355
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9586344
X-RAY DIFFRACTIONr_angle_other_deg1.014310030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7385607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32524.641181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01315741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.001159
X-RAY DIFFRACTIONr_chiral_restr0.080.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215337
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021060
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.14.352437
X-RAY DIFFRACTIONr_mcbond_other3.0994.3492436
X-RAY DIFFRACTIONr_mcangle_it4.2826.5013038
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9534.7592253
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.185→2.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 166 -
Rwork0.244 2830 -
obs--100 %

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