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Yorodumi- PDB-2qmm: Crystal structure of APC86534.1 (C-terminal domain of NCBI AAB901... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qmm | ||||||
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Title | Crystal structure of APC86534.1 (C-terminal domain of NCBI AAB90184.1; Pfam BIG 123.1) | ||||||
Components | UPF0217 protein AF_1056 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha/beta knot / SAM / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information tRNA (pseudouridine54-N1)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus DSM 4304 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | ||||||
Authors | Joachimiak, A. / Duke, N. / Zhou, M. / Gu, M. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of APC86534.1 (C-terminal domain of NCBI AAB90184.1; Pfam BIG 123.1). Authors: Joachimiak, A. / Duke, N. / Zhou, M. / Gu, M. | ||||||
History |
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Remark 600 | HETEROGEN AUTHORS STATE THAT THE STRUCTURE CONTAINS CO-FACTOR WHICH IS ALMOST CERTAINLY SAM, BUT ... HETEROGEN AUTHORS STATE THAT THE STRUCTURE CONTAINS CO-FACTOR WHICH IS ALMOST CERTAINLY SAM, BUT IT HAS MISSING ATOMS DUE TO LACK OF ELECTRON DENSITY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qmm.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qmm.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qmm ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qmm | HTTPS FTP |
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-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: 21910.326 Da / Num. of mol.: 2 / Fragment: C-terminal domain: Residues 95-288 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Species: Archaeoglobus fulgidus / Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126 / Gene: AF_1056 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: O29206 #2: Chemical | #3: 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: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 25% PEG 3350 (Hampton Research Index, condition 44), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2006 / Details: bent mirror |
Radiation | Monochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 50772 / Num. obs: 49604 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 19.926 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 33.3 |
Reflection shell | Resolution: 1.85→1.87 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.97 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→43.94 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.522 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.122 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.097 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→43.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.9 Å / Total num. of bins used: 20
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