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- PDB-2pby: Probable Glutaminase from Geobacillus kaustophilus HTA426 -

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Basic information

Entry
Database: PDB / ID: 2pby
TitleProbable Glutaminase from Geobacillus kaustophilus HTA426
ComponentsGlutaminase
KeywordsHYDROLASE / Glutaminase / SECSG / RIKEN / Structural Genomics / PSI / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Southeast Collaboratory for Structural Genomics
Function / homology
Function and homology information


glutaminase / glutaminase activity / glutamine metabolic process
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
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsDillard, B.D. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Rose, J.P. / Wang, B.-C. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Glutaminase from Geobacillus kaustophilus HTA426
Authors: Dillard, B.D. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Rose, J.P. / Wang, B.-C.
History
DepositionMar 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaminase
B: Glutaminase
C: Glutaminase
D: Glutaminase


Theoretical massNumber of molelcules
Total (without water)135,2404
Polymers135,2404
Non-polymers00
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-50 kcal/mol
Surface area44110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.503, 86.786, 106.881
Angle α, β, γ (deg.)90.00, 109.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutaminase


Mass: 33810.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK2125 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5KY26, glutaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: 20% PEG 4000, 0.08 M Na Acetate pH 4.6, 0.16 M Ammonium Sulfate, 20% Glycerol, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 13, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 18.1 / Number: 231597 / Rmerge(I) obs: 0.053 / Χ2: 1.76 / D res high: 2.08 Å / D res low: 50 Å / Num. obs: 69859 / % possible obs: 93.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.485090.510.0281.3473.5
3.564.4893.510.0422.4433.4
3.113.5694.910.0462.0623.4
2.823.1195.410.0592.0953.3
2.622.8295.710.071.8673.3
2.472.6295.510.0861.6463.3
2.342.4794.610.0991.5633.3
2.242.3493.310.1231.643.3
2.152.2493.310.1521.4283.3
2.082.1588.310.1771.3573.1
ReflectionResolution: 2.07→50 Å / Num. obs: 75938 / % possible obs: 93.5 % / Redundancy: 3.3 % / Rsym value: 0.053 / Χ2: 1.756 / Net I/σ(I): 18.1
Reflection shellResolution: 2.07→2.15 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 7.38 / Num. unique all: 6535 / Rsym value: 0.177 / Χ2: 1.357 / % possible all: 88.3

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Phasing

Phasing MRRfactor: 0.598 / Cor.coef. Fo:Fc: 0.164
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MKI

1mki


Resolution: 2.07→19.86 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.846 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3706 5 %RANDOM
Rwork0.195 ---
all0.198 75938 --
obs0.198 73873 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.994 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.07→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8795 0 0 515 9310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0228921
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.99112050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36251147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95324.083360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.721151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4871563
X-RAY DIFFRACTIONr_chiral_restr0.1650.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026575
X-RAY DIFFRACTIONr_nbd_refined0.2260.24183
X-RAY DIFFRACTIONr_nbtor_refined0.3080.26361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2434
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.218
X-RAY DIFFRACTIONr_mcbond_it1.9261.55950
X-RAY DIFFRACTIONr_mcangle_it2.07229198
X-RAY DIFFRACTIONr_scbond_it3.87233369
X-RAY DIFFRACTIONr_scangle_it6.0314.52852
LS refinement shellResolution: 2.07→2.123 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 204 -
Rwork0.198 4053 -
obs-4257 76.9 %

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