+Open data
-Basic information
Entry | Database: PDB / ID: 2d5a | |||||||||
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Title | hypothetical protein from Pyrococcus horikoshii OT3 | |||||||||
Components | hypothetical protein PH1109 | |||||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / coa binding / hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pyrococcus horikoshii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Hiyama, T.B. / Sekine, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2006 Title: Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins. Authors: Hiyama, T.B. / Zhao, M. / Kitago, Y. / Yao, M. / Sekine, S. / Terada, T. / Kuroishi, C. / Liu, Z.J. / Rose, J.P. / Kuramitsu, S. / Shirouzu, M. / Watanabe, N. / Yokoyama, S. / Tanaka, I. / Wang, B.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d5a.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d5a.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 2d5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d5a_validation.pdf.gz | 706.2 KB | Display | wwPDB validaton report |
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Full document | 2d5a_full_validation.pdf.gz | 711.7 KB | Display | |
Data in XML | 2d5a_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 2d5a_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/2d5a ftp://data.pdbj.org/pub/pdb/validation_reports/d5/2d5a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16747.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: ph1109 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58836 |
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#2: Chemical | ChemComp-COA / |
#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: 3.09 Å3/Da / Density % sol: 60.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% PEG 4000, 0.1M Tris-HCl, 0.2M Sodium Fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2005 |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 23416 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 17.2 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 31.919 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2041 / Rsym value: 0.639 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→37.48 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 255040.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.1413 Å2 / ksol: 0.381238 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→37.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file |
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