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- PDB-3if5: Crystal Structure Analysis of Mglu -

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Basic information

Entry
Database: PDB / ID: 3if5
TitleCrystal Structure Analysis of Mglu
ComponentsSalt-tolerant glutaminase
KeywordsHYDROLASE / Fragment
Function / homology
Function and homology information


glutaminase / glutaminase activity / glutamine metabolic process
Similarity search - Function
STAS domain / Glutaminase / Glutaminase / Transcription Regulator spoIIAA / STAS domain profile. / STAS domain / STAS domain superfamily / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like ...STAS domain / Glutaminase / Glutaminase / Transcription Regulator spoIIAA / STAS domain profile. / STAS domain / STAS domain superfamily / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMicrococcus luteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.44 Å
AuthorsYoshimune, K. / Shirakihara, Y.
Citation
Journal: Febs J. / Year: 2010
Title: Crystal structure of salt-tolerant glutaminase from Micrococcus luteus K-3 in the presence and absence of its product L-glutamate and its activator Tris.
Authors: Yoshimune, K. / Shirakihara, Y. / Wakayama, M. / Yumoto, I.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Crystal structure of a major fragment of the salt-tolerant glutaminase from Micrococcus luteus K-3
Authors: Yoshimune, K. / Shirakihara, Y. / Shiratori, A. / Wakayama, M. / Chantawannakul, P. / Moriguchi, M.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 4, 2009ID: 2DFW
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Salt-tolerant glutaminase


Theoretical massNumber of molelcules
Total (without water)48,3041
Polymers48,3041
Non-polymers00
Water2,072115
1
A: Salt-tolerant glutaminase

A: Salt-tolerant glutaminase


Theoretical massNumber of molelcules
Total (without water)96,6072
Polymers96,6072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6220 Å2
ΔGint-24 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.331, 116.680, 144.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Salt-tolerant glutaminase


Mass: 48303.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrococcus luteus (bacteria) / Strain: K-3 / Gene: Glutaminase / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q4U1A6, glutaminase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 700mM Sodium Citrate, 50mM HEPES, 5mM MgCl2, 5% Glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9791, 0.9793, 0.9700
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2001
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.971
ReflectionResolution: 2.4→36.18 Å / Num. all: 18367 / Num. obs: 17155 / Redundancy: 6.8 % / Biso Wilson estimate: 38.9 Å2

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.44→36.18 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 0.67 / Data cutoff high absF: 6969453 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 863 5 %RANDOM
Rwork0.204 ---
obs-17155 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.196 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 110.85 Å2 / Biso mean: 39.072 Å2 / Biso min: 2.42 Å2
Baniso -1Baniso -2Baniso -3
1-4.78 Å20 Å20 Å2
2--9.67 Å20 Å2
3----14.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.44→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 0 115 3097
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it2.381.5
X-RAY DIFFRACTIONc_mcangle_it42
X-RAY DIFFRACTIONc_scbond_it3.992
X-RAY DIFFRACTIONc_scangle_it6.492.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 68 5.4 %
Rwork0.233 1196 -
all-1264 -
obs--40 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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