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Yorodumi- PDB-1nog: Crystal Structure of Conserved Protein 0546 from Thermoplasma Aci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nog | ||||||
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Title | Crystal Structure of Conserved Protein 0546 from Thermoplasma Acidophilum | ||||||
Components | conserved hypothetical protein TA0546 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å | ||||||
Authors | Saridakis, V. / Sanishvili, R. / Iakounine, A. / Xu, X. / Pennycooke, M. / Gu, J. / Joachimiak, A. / Arrowsmith, C.H. / Edwards, A.M. / Christendat, D. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The structural basis for methylmalonic aciduria. The crystal structure of archaeal ATP:cobalamin adenosyltransferase. Authors: Saridakis, V. / Yakunin, A. / Xu, X. / Anandakumar, P. / Pennycooke, M. / Gu, J. / Cheung, F. / Lew, J.M. / Sanishvili, R. / Joachimiak, A. / Arrowsmith, C.H. / Christendat, D. / Edwards, A.M. | ||||||
History |
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Remark 999 | SEQUENCE The authors state that According to the density, the residue at position 110 is valine and ...SEQUENCE The authors state that According to the density, the residue at position 110 is valine and the residue at position 159 is ile. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nog.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nog.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/1nog ftp://data.pdbj.org/pub/pdb/validation_reports/no/1nog | 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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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by crystallographic symmetry. |
-Components
#1: Protein | Mass: 20029.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: TA1434 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HIA7 |
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#2: 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: 2.94 Å3/Da / Density % sol: 58.18 % | |||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.4 M ammonium phosphate, 6 % methylpentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop / Details: Christendat, D., (2000) J.Biol.Chem., 275, 24608. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 14, 2001 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 34479 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.55→1.6 Å / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3233 / % possible all: 100 |
Reflection | *PLUS Num. obs: 62540 / % possible obs: 99 % / Num. measured all: 341835 / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.47 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.55→29.69 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.7177 Å2 / ksol: 0.378784 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze | Luzzati coordinate error free: 0.19 Å / Luzzati sigma a free: 0.13 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→29.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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