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Yorodumi- PDB-2f4n: Crystal structure of protein MJ1651 from Methanococcus jannaschii... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f4n | ||||||
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Title | Crystal structure of protein MJ1651 from Methanococcus jannaschii DSM 2661, Pfam DUF62 | ||||||
Components | Hypothetical protein MJ1651Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein / Mehtanococcus jannaschii / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information Transferases; Transferring alkyl or aryl groups, other than methyl groups / transferase activity Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Rao, K.N. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii. Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f4n.cif.gz | 144.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f4n.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 2f4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/2f4n ftp://data.pdbj.org/pub/pdb/validation_reports/f4/2f4n | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31655.486 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ1651 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59045 #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: 2.52 Å3/Da / Density % sol: 51.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50% MPD, 0.2M Ammonium dihydrogen phosphate, pH 8.0, 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: 0.9789 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2005 / Details: mirrors |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→39.86 Å / Num. all: 72852 / Num. obs: 72852 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.36→2.45 Å / Redundancy: 4 % / Rmerge(I) obs: 0.465 / Num. unique all: 3261 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→39.86 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The missing atoms (Remark 470) and missing residues (Remark 465) are due to lack of or weak electron density.
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Displacement parameters | Biso mean: 38.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→39.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 2.7
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