+Open data
-Basic information
Entry | Database: PDB / ID: 4amq | ||||||
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Title | A Megaviridae Orfan gene encodes a new nucleotidyl transferase | ||||||
Components | L544 | ||||||
Keywords | TRANSFERASE / MIMIVIRUS / MG662 / TRANSCRIPTION COUPLED DNA REPAIR | ||||||
Function / homology | virion component => GO:0044423 / : / Uncharacterized protein L544 Function and homology information | ||||||
Biological species | ACANTHAMOEBA POLYPHAGA MIMIVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.17 Å | ||||||
Authors | Lartigue, A. / Claverie, J.M. / Priet, S. / Abergel, C. | ||||||
Citation | Journal: To be Published Title: A Megaviridae Orphan Gene Encodes a New Nucleotidyl Transferase Authors: Ciaccafava, A. / Lartigue, A. / Mansuelle, P. / Jeudy, S. / Abergel, C. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Preliminary Crystallographic Analysis of a Possible Transcription Factor Encoded by the Mimivirus L544 Gene. Authors: Ciaccafava, A. / Lartigue, A. / Mansuelle, P. / Jeudy, S. / Abergel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4amq.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4amq.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 4amq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4amq ftp://data.pdbj.org/pub/pdb/validation_reports/am/4amq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 48334.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACANTHAMOEBA POLYPHAGA MIMIVIRUS / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q5UQA5 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Nonpolymer details | MANGANESE (II) ION (MN): LOCATED IN THE NUCLEOTIDY | Sequence details | ADDITIONAL N-TERMINAL HIS-TAG, LEU -1 REPLACES INITIATION METHIONINE. NUCLEOTIDYL TRANSFERASE ...ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.58 % |
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Crystal grow | pH: 6 Details: PROTEIN CONCENTRATION: 10 MG/ML IN 10 MM CHES BUFFER PH 9.0 RESERVOIR: 4 TO 12% PEG 4000, 0.1 M SODIUM CACODYLATE BETWEEN PH 6 AND 7, 0.1 M MNCL2 |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97918 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50.4 Å / Num. obs: 20963 / % possible obs: 96 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.17→2.25 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.17→29.29 Å / SU ML: 0.31 / σ(F): 0.03 / Phase error: 25.6 / Stereochemistry target values: ML Details: - LOOP RESIDUES 120 TO 126 ARE DISORDERED - LINKER RESIDUES 198 TO 210 ARE DISORDERED - RESIDUES 360 TO THE END ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.034 Å2 / ksol: 0.363 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→29.29 Å
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Refine LS restraints |
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LS refinement shell |
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