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- PDB-3agd: Crystal structure of Mglu in its native form in the presence of 4... -

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Basic information

Entry
Database: PDB / ID: 3agd
TitleCrystal structure of Mglu in its native form in the presence of 4.3M NaCl
ComponentsSalt-tolerant glutaminase
KeywordsHYDROLASE / Glutaminase super family
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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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
Water13,872770
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-46 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.808, 131.150, 73.175
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 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 / Water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 293 K / Method: microbatch method / pH: 7.5
Details: 10mg/ml protein, 50mM HEPES, 1M ammonium formate, 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: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→62.3 Å / Num. all: 58860 / Num. obs: 58857 / % possible obs: 100 % / Observed criterion σ(I): 4.8 / Redundancy: 6.8 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 17.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.8 / Num. unique all: 8473 / Rsym value: 0.381 / % 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 3if5

3if5


Resolution: 2.2→59.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2950 5 %RANDOM
Rwork0.194 55843 --
all-58809 --
obs-58793 100 %-
Displacement parametersBiso mean: 29.493 Å2
Baniso -1Baniso -2Baniso -3
1-5.306 Å20 Å20 Å2
2---1.501 Å20 Å2
3----3.804 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→59.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6513 0 0 770 7283
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it2.0241.5
X-RAY DIFFRACTIONc_scbond_it3.592
X-RAY DIFFRACTIONc_mcangle_it3.2720
X-RAY DIFFRACTIONc_scangle_it5.56920.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.2-2.30.3013930.2680.015724399.6
2.3-2.420.253760.2150.013726099.8
2.42-2.570.2523710.2030.013724599.9
2.57-2.770.2683490.220.014731299.9
2.77-3.050.2523510.2170.013731599.9
3.05-3.490.2353560.1950.012734599.9
3.49-4.40.1843540.1540.01739099.9
4.4-59.40.2324000.1780.0127683100

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