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- PDB-7d54: Crstal structure MsGATase with Gln -

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Basic information

Entry
Database: PDB / ID: 7d54
TitleCrstal structure MsGATase with Gln
ComponentsGlutamine amidotransferase class-I
KeywordsTRANSFERASE / MsGATase / glutamine amidotransferase / Class I GAT family / Mycolicibacterium smegmatis.
Function / homologyGLUTAMINE
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChen, Y. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
National Natural Science Foundation of China (NSFC)31800627 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structure and mechanism of the gamma-glutamyl-gamma-aminobutyrate hydrolase SpuA from Pseudomonas aeruginosa.
Authors: Chen, Y. / Jia, H. / Zhang, J. / Liang, Y. / Liu, R. / Zhang, Q. / Bartlam, M.
History
DepositionSep 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Glutamine amidotransferase class-I
B: Glutamine amidotransferase class-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6604
Polymers53,3682
Non-polymers2922
Water9,656536
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-3 kcal/mol
Surface area19950 Å2
Unit cell
Length a, b, c (Å)69.376, 72.494, 69.529
Angle α, β, γ (deg.)90.000, 111.370, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glutamine amidotransferase class-I


Mass: 26684.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The GlU-1 and PHE0 are from the tag. / Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: guaA_2, ERS451418_04095 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GMP synthase (glutamine-hydrolysing)
#2: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS WP_011729647. FOR THE PROTEIN.

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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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 2.0M Ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 54049 / % possible obs: 98.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 26.82 Å2 / Rpim(I) all: 0.068 / Net I/σ(I): 18.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2708 / Rpim(I) all: 0.334 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O1Y

1o1y


Resolution: 1.85→36.25 Å / SU ML: 0.217 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 1997 3.7 %
Rwork0.1923 51995 -
obs0.1939 53992 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.07 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 20 536 4314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01243874
X-RAY DIFFRACTIONf_angle_d1.1915282
X-RAY DIFFRACTIONf_chiral_restr0.0606574
X-RAY DIFFRACTIONf_plane_restr0.008698
X-RAY DIFFRACTIONf_dihedral_angle_d11.5532524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.29571330.25063445X-RAY DIFFRACTION91.56
1.89-1.950.40041430.32013701X-RAY DIFFRACTION99.33
1.95-20.25621450.21443792X-RAY DIFFRACTION99.77
2-2.070.28261410.20983728X-RAY DIFFRACTION99.79
2.07-2.140.2471460.19143786X-RAY DIFFRACTION99.49
2.14-2.230.24731410.19883740X-RAY DIFFRACTION98.93
2.23-2.330.26051400.21223715X-RAY DIFFRACTION98.49
2.33-2.450.23031440.18283725X-RAY DIFFRACTION99.43
2.45-2.610.20691430.18353742X-RAY DIFFRACTION99.03
2.61-2.810.23941430.1923745X-RAY DIFFRACTION98.91
2.81-3.090.27591440.20363706X-RAY DIFFRACTION98.42
3.09-3.540.23321410.19113717X-RAY DIFFRACTION97.6
3.54-4.450.19351440.16293654X-RAY DIFFRACTION96.03
4.45-36.250.21571490.18463799X-RAY DIFFRACTION97.7

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