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Yorodumi- PDB-3gmi: Crystal structure of a protein of unknown function from Methanoca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gmi | ||||||
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Title | Crystal structure of a protein of unknown function from Methanocaldococcus jannaschii | ||||||
Components | UPF0348 protein MJ0951 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein with unknown function / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #620 / Putative cytidyltransferase-related, C-terminal region / Cytidyltransferase-related C-terminal region / tRNA(Met) cytidine acetate ligase / HIGH Nucleotidyl Transferase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Rossmann fold ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #620 / Putative cytidyltransferase-related, C-terminal region / Cytidyltransferase-related C-terminal region / tRNA(Met) cytidine acetate ligase / HIGH Nucleotidyl Transferase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Zhang, R. / Hatzos, C. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the protein with unknown function from Methanocaldococcus jannaschii Authors: Zhang, R. / Hatzos, C. / Freeman, L. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gmi.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gmi.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gmi_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 3gmi_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 3gmi_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 3gmi_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gmi ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gmi | 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: 41587.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Gene: GI:1591618, MJ0951 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q58361 |
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#2: Chemical | ChemComp-MLI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.15 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2M Lithium chloride, 0.05M Magnesium sulfate, 8% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Jun 17, 2008 / Details: Mirrors |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→55.81 Å / Num. all: 33730 / Num. obs: 33426 / % possible obs: 99.1 % / Observed criterion σ(I): 1.3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.91→1.96 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.27 / Num. unique all: 2546 / % possible all: 89.71 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→55.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.098 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.123 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.353 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→55.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.96 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 41.318 Å / Origin y: 16.399 Å / Origin z: 10.587 Å
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Refinement TLS group |
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