+Open data
-Basic information
Entry | Database: PDB / ID: 4ams | ||||||
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Title | A Megaviridae ORFan gene encode a new nucleotidyl transferase | ||||||
Components | MG662 | ||||||
Keywords | TRANSFERASE / MIMIVIRUS / TRANSCRIPTION COUPLED DNA REPAIR | ||||||
Function / homology | : / : / L544, nucleotidyltransferase domain / Nucleotidyl transferase L544, helical domain / GTP binding / metal ion binding / Uncharacterized protein mg662 Function and homology information | ||||||
Biological species | MEGAVIRUS CHILIENSIS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 4ams.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ams.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ams.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ams_validation.pdf.gz | 433.4 KB | Display | wwPDB validaton report |
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Full document | 4ams_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 4ams_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4ams_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4ams ftp://data.pdbj.org/pub/pdb/validation_reports/am/4ams | HTTPS FTP |
-Related structure data
Related structure data | 4amqSC 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: 46165.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MEGAVIRUS CHILIENSIS / Plasmid: MODIFIED PETDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: G5CQN7 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | ADDITIONAL N-TERMINAL HIS-TAG, SER 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: 4.62 Å3/Da / Density % sol: 73.43 % |
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Crystal grow | pH: 6 Details: PROTEIN CONCENTRATION: 5 TO 12 MG/ML IN 10 MM CAPS BUFFER, 150 MM NACL, PH 10.5 RESERVOIR SOLUTION: 150 MM NA ACETATE PH 6 |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→24.6 Å / Num. obs: 26030 / % possible obs: 99.8 % / Redundancy: 8.2 % / Biso Wilson estimate: 65.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.48 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AMQ Resolution: 2.6→24.558 Å / SU ML: 0.32 / σ(F): 0.02 / Phase error: 24.61 / 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 / Bsol: 42.331 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→24.558 Å
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Refine LS restraints |
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LS refinement shell |
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