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Yorodumi- PDB-2q5z: Crystal structure of iMazG from Vibrio DAT 722: Ntag-iMazG (P43212) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q5z | ||||||
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Title | Crystal structure of iMazG from Vibrio DAT 722: Ntag-iMazG (P43212) | ||||||
Components | Hypothetical protein | ||||||
Keywords | HYDROLASE / MazG / Vibrio / NTP-PPase | ||||||
Function / homology | NTP pyrophosphohydrolase MazG, putative catalytic core / MazG nucleotide pyrophosphohydrolase domain / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / metal ion binding / NTP pyrophosphohydrolase MazG-like domain-containing protein Function and homology information | ||||||
Biological species | Vibrio sp. DAT722 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Robinson, A. / Guilfoyle, A.P. / Harrop, S.J. / Boucher, Y. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2007 Title: A putative house-cleaning enzyme encoded within an integron array: 1.8 A crystal structure defines a new MazG subtype. Authors: Robinson, A. / Guilfoyle, A.P. / Harrop, S.J. / Boucher, Y. / Stokes, H.W. / Curmi, P.M. / Mabbutt, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q5z.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q5z.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 2q5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q5z_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 2q5z_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 2q5z_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2q5z_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/2q5z ftp://data.pdbj.org/pub/pdb/validation_reports/q5/2q5z | HTTPS FTP |
-Related structure data
Related structure data | 2q73C 2q9lC 1vmgS C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 1 - 90 / Label seq-ID: 21 - 110
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Details | The second part of the biological assembly is generated by the operation: Y, X, -Z, 0, 0, 1 |
-Components
#1: Protein | Mass: 13095.751 Da / Num. of mol.: 2 / Mutation: H81R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio sp. DAT722 (bacteria) / Strain: DAT 722 / Gene: imazG / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS References: UniProt: Q2F9Z1, nucleoside-triphosphate diphosphatase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.12 Å3/Da / Density % sol: 60.63 % |
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Crystal grow | Temperature: 293 K / pH: 5.5 Details: 0.1 M sodium citrate, 8% PEG 8000, 0.1M NaCl, pH 5.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 28, 2005 / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→17.173 Å / Num. obs: 15523 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 32.1 % / Rmerge(I) obs: 0.099 / Rsym value: 0.098 / Net I/σ(I): 39.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 32.7 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 9 / Rsym value: 0.483 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VMG Resolution: 2.3→17.17 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.152 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→17.17 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 711 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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