+Open data
-Basic information
Entry | Database: PDB / ID: 7d54 | |||||||||
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Title | Crstal structure MsGATase with Gln | |||||||||
Components | Glutamine amidotransferase class-I | |||||||||
Keywords | TRANSFERASE / MsGATase / glutamine amidotransferase / Class I GAT family / Mycolicibacterium smegmatis. | |||||||||
Function / homology | GLUTAMINE Function and homology information | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Chen, Y. / Zhang, Q. / Bartlam, M. | |||||||||
Funding support | China, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d54.cif.gz | 239 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d54.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 7d54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d54_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7d54_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7d54_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 7d54_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/7d54 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/7d54 | HTTPS FTP |
-Related structure data
Related structure data | 7d4rC 7d50C 7d53C 1o1yS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | THE 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 KNOWLEDGEB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 2.0M Ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→36.25 Å
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Refine LS restraints |
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LS refinement shell |
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