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- PDB-3ihb: Crystal Structure Analysis of Mglu in its tris and glutamate form -

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Basic information

Entry
Database: PDB / ID: 3ihb
TitleCrystal Structure Analysis of Mglu in its tris and glutamate 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
GLUTAMIC ACID / Glutaminase
Similarity search - Component
Biological speciesMicrococcus luteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Salt-tolerant glutaminase
B: Salt-tolerant glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1466
Polymers96,6072
Non-polymers5394
Water9,206511
1
A: Salt-tolerant glutaminase
hetero molecules

A: Salt-tolerant glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1466
Polymers96,6072
Non-polymers5394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9440 Å2
ΔGint-31 kcal/mol
Surface area32970 Å2
MethodPISA
2
B: Salt-tolerant glutaminase
hetero molecules

B: Salt-tolerant glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1466
Polymers96,6072
Non-polymers5394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9440 Å2
ΔGint-35 kcal/mol
Surface area32730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.359, 141.202, 76.115
Angle α, β, γ (deg.)90.000, 105.370, 90.000
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: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 15% PEG 4000, 100mM Sodium Acetate, 50mM HEPES, 300mM Tris, 200mM Glutamate, pH 7.2, 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: Feb 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→57.073 Å / Num. obs: 46819 / % possible obs: 99.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 4.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.412 / % possible all: 98.6

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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 3IH8

3ih8


Resolution: 2.4→19.86 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.67 / Data cutoff high absF: 2131955 / 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
Rfree0.268 2305 4.9 %RANDOM
Rwork0.221 ---
obs-46741 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.711 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 116.63 Å2 / Biso mean: 40.938 Å2 / Biso min: 7.6 Å2
Baniso -1Baniso -2Baniso -3
1--10.27 Å20 Å2-2.4 Å2
2---4.11 Å20 Å2
3---14.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6677 0 34 511 7222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 390 5.1 %
Rwork0.31 7311 -
all-7701 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3gluTMN_xplor_par.txtgluTMN_xplor_top.txt

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