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- PDB-3ih8: Crystal Structure Analysis of Mglu in its native form -

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Basic information

Entry
Database: PDB / ID: 3ih8
TitleCrystal Structure Analysis of Mglu in its native form
ComponentsSalt-tolerant glutaminase
KeywordsHYDROLASE / Salt-tolerant glutaminase
Function / homology
Function and homology information


L-glutamine catabolic process / glutamate biosynthetic process / glutaminase / glutaminase activity
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsYoshimune, K. / Shirakihara, Y.
CitationJournal: 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.
History
DepositionJul 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: 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

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Assembly

Deposited unit
A: Salt-tolerant glutaminase
B: Salt-tolerant glutaminase


Theoretical massNumber of molelcules
Total (without water)96,6072
Polymers96,6072
Non-polymers00
Water7,800433
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_555-x,y,-z1
Buried area7630 Å2
ΔGint-40 kcal/mol
Surface area29300 Å2
MethodPISA
2
B: Salt-tolerant glutaminase

B: 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_555-x,y,-z1
Buried area7390 Å2
ΔGint-40 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.076, 142.251, 74.248
Angle α, β, γ (deg.)90.00, 104.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Salt-tolerant glutaminase


Mass: 48303.516 Da / Num. of mol.: 2
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


Mass: 18.015 Da / Num. of mol.: 433 / 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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 4000, 100mM Sodium Acetate, 50mM HEPES, pH 7.5, vapor diffusion, hanging drop, 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: May 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→62.137 Å / Num. obs: 52671 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 10.9 / Num. measured all: 189811
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.423.60.5461.42722776590.54699.9
2.42-2.573.60.37122643572730.371100
2.57-2.753.60.2732.62480768110.273100
2.75-2.973.60.18142322863790.181100
2.97-3.253.60.1295.22117058080.129100
3.25-3.643.60.0986.51932753200.098100
3.64-4.23.60.0877.11667546880.087100
4.2-5.143.60.0688.41427839610.068100
5.14-7.273.60.078.51095430600.07100
7.27-62.143.30.0618.8571017120.06199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
AMoREphasing
CNS1.2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IF5

3if5


Resolution: 2.3→19.9 Å / Occupancy max: 1.43 / Occupancy min: 0.67 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2620 5 %RANDOM
Rwork0.247 ---
obs-52579 99.8 %-
Solvent computationBsol: 80.094 Å2
Displacement parametersBiso max: 120.01 Å2 / Biso mean: 40.782 Å2 / Biso min: 11.39 Å2
Baniso -1Baniso -2Baniso -3
1--6.207 Å20 Å21.339 Å2
2---3.103 Å20 Å2
3---9.309 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 0 433 6549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.294
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION315p_xplor_par.txt

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