+Open data
-Basic information
Entry | Database: PDB / ID: 7vf6 | ||||||
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Title | The crystal structure of PurZ0 | ||||||
Components | PurA-like adenylosuccinate synthetase | ||||||
Keywords | LIGASE / PurA-like adenylosuccinate synthetase | ||||||
Function / homology | Function and homology information 2-amino-2'-deoxyadenylo-succinate synthase / adenylosuccinate synthase activity / purine nucleotide biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Gordonia phage Archimedes (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å | ||||||
Authors | Tong, Y. / Zhang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Microbiol / Year: 2023 Title: Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage. Authors: Tong, Y. / Wu, X. / Liu, Y. / Chen, H. / Zhou, Y. / Jiang, L. / Li, M. / Zhao, S. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vf6.cif.gz | 169.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vf6.ent.gz | 130.4 KB | Display | PDB format |
PDBx/mmJSON format | 7vf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vf6_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 7vf6_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 7vf6_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 7vf6_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/7vf6 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/7vf6 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40489.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gordonia phage Archimedes (virus) / Gene: 50, SEA_ARCHIMEDES_50 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7L7SI10 |
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-Non-polymers , 5 types, 596 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.25 Å3/Da / Density % sol: 45.42 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 1.26M ammonium sulfate, 0.2M lithium sulfate, 0.1M Tris, pH 8.5, 5mM GTP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. obs: 78554 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 12.64 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.068 / Rrim(I) all: 0.159 / Χ2: 0.92 / Net I/σ(I): 6.7 / Num. measured all: 427033 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Phyre2 prediction structure Resolution: 1.703→37.895 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.14 / Stereochemistry target values: ML
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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 max: 61.84 Å2 / Biso mean: 15.595 Å2 / Biso min: 3.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.703→37.895 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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