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- PDB-3agf: Crystal structure of Bacillus glutaminase in the presence of 4.3M NaCl -

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Basic information

Entry
Database: PDB / ID: 3agf
TitleCrystal structure of Bacillus glutaminase in the presence of 4.3M NaCl
ComponentsGlutaminase 1
KeywordsHYDROLASE / Glutaminase super family
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
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYoshimune, K. / Shirakihara, Y. / Yumoto, I.
CitationJournal: To be Published
Title: Salt-induced conformational change of salt-tolerant glutaminase from Micrococcus luteus K-3
Authors: Yoshimune, K. / Shirakihara, Y. / Yumoto, I.
History
DepositionMar 30, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1
B: Glutaminase 1


Theoretical massNumber of molelcules
Total (without water)72,4492
Polymers72,4492
Non-polymers00
Water4,288238
1
A: Glutaminase 1
B: Glutaminase 1

A: Glutaminase 1
B: Glutaminase 1


Theoretical massNumber of molelcules
Total (without water)144,8984
Polymers144,8984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7630 Å2
ΔGint-45 kcal/mol
Surface area40650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.837, 179.965, 51.878
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: 36224.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: Glutaminase / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O31465, glutaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293 K / Method: microbatch method / pH: 7.5
Details: 11mg/ml protein, 50mM HEPES, 4.3M NaCl, pH 7.5, Microbatch method, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→19.82 Å / Num. all: 21097 / Num. obs: 21093 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.191 / Rsym value: 0.191 / Net I/σ(I): 8.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3037 / Rsym value: 0.55 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1mki

1mki


Resolution: 2.6→19.8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1064 5 %RANDOM
Rwork0.213 20029 --
all-21097 --
obs-21093 100 %-
Solvent computationBsol: 45.256 Å2
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1--13.51 Å20 Å20 Å2
2---2.83 Å20 Å2
3---16.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4623 0 0 238 4861
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it2.2961.5
X-RAY DIFFRACTIONc_scbond_it3.5182
X-RAY DIFFRACTIONc_mcangle_it3.82420
X-RAY DIFFRACTIONc_scangle_it5.46520.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.6-2.720.3711180.3240.034256999.7
2.72-2.860.3451360.2970.03260299.7
2.86-3.040.2891380.2720.0252579100
3.04-3.270.2751310.2290.024261599.8
3.27-3.60.2661390.2110.023261099.9
3.6-4.120.1961160.1970.018263199.9
4.12-5.170.191390.1760.0162691100
5.17-19.820.2511470.210.0212796100

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