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Yorodumi- PDB-4dpo: Crystal structure of a conserved protein MM_1583 from Methanosarc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dpo | ||||||
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Title | Crystal structure of a conserved protein MM_1583 from Methanosarcina mazei Go1 | ||||||
Components | Conserved protein | ||||||
Keywords | UNKNOWN FUNCTION / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Putative antibitic biosynthesis mono oxygenase | ||||||
Function / homology | ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Conserved protein Function and homology information | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å | ||||||
Authors | Agarwal, R. / Chamala, S. / Evans, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Foti, R. / Siedel, R. / Zencheck, W. ...Agarwal, R. / Chamala, S. / Evans, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Foti, R. / Siedel, R. / Zencheck, W. / Villigas, G. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a conserved protein MM_1583 from Methanosarcina mazei Go1 Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dpo.cif.gz | 48.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dpo.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 4dpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dpo_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 4dpo_full_validation.pdf.gz | 446.2 KB | Display | |
Data in XML | 4dpo_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 4dpo_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/4dpo ftp://data.pdbj.org/pub/pdb/validation_reports/dp/4dpo | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14249.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: MM_1583 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8PWK2 #2: 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: 3.29 Å3/Da / Density % sol: 62.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris, pH 8.5, 2M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2012 / Details: Mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→50 Å / Num. all: 10299 / Num. obs: 10299 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.71→2.81 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 5 / Num. unique all: 1024 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: None Resolution: 2.73→39.43 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.305 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.436 / ESU R Free: 0.316 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.73→39.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.726→2.797 Å / Total num. of bins used: 20
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