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- PDB-2osu: Probable glutaminase from Bacillus subtilis complexed with 6-diaz... -

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Basic information

Entry
Database: PDB / ID: 2osu
TitleProbable glutaminase from Bacillus subtilis complexed with 6-diazo-5-oxo-L-norleucine
ComponentsGlutaminase 1
KeywordsHYDROLASE / alpha-beta structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


L-glutamine catabolic process / glutamate biosynthetic process / glutaminase / glutaminase activity
Similarity search - Function
Probable Glutaminase Ybgj; Chain: A, domain 2 / Probable Glutaminase Ybgj; Chain: A, domain 2 - #10 / Glutaminase / Glutaminase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-DIAZENYL-5-OXO-L-NORLEUCINE / Glutaminase 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsKim, Y. / Dementieva, I. / Vinokour, E. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of probable glutaminase from B. subtilis complexed with its inhibitor 6-diazo-5-oxo-L-norleucine
Authors: Kim, Y. / Dementieva, I. / Vinokour, E. / Collart, F. / Joachimiak, A.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Glutaminase 1
B: Glutaminase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4654
Polymers74,1192
Non-polymers3462
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.247, 184.701, 51.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glutaminase 1


Mass: 37059.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: glsA1, glsA, BSU02430 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O31465, glutaminase
#2: Chemical ChemComp-DON / 6-DIAZENYL-5-OXO-L-NORLEUCINE / (S)-2-AMINO-6-DIAZENYL-5-OXOHEXANOIC ACID


Type: L-peptide linking / Mass: 173.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14.5% PEG1500, 12% Glycerol, 500 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 15, 2004 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→34.52 Å / Num. all: 30785 / Num. obs: 30785 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 5.2
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 1.91 / Num. unique all: 2616 / % possible all: 83.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→34.52 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 14.674 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.379 / ESU R Free: 0.257
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: positions of DON atoms are only about 60 % confident
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3076 10 %RANDOM
Rwork0.194 ---
all0.2 27646 --
obs0.2 27646 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.281 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2---0.22 Å20 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.29→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 24 232 5030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224911
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.976659
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9445617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45124.515206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91915824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9471520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023722
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.22219
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23406
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8851.53168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3224946
X-RAY DIFFRACTIONr_scbond_it2.05832000
X-RAY DIFFRACTIONr_scangle_it3.174.51713
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 165 -
Rwork0.226 1567 -
obs-1732 81.31 %

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