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Yorodumi- PDB-1q89: Crystal structure of the C-domain of the T.vaginalis Inr binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q89 | ||||||
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Title | Crystal structure of the C-domain of the T.vaginalis Inr binding protein, IBP39 (cubic crystal form) | ||||||
Components | 39 kDa initiator binding protein | ||||||
Keywords | DNA BINDING PROTEIN / Inr / initator binding protein / core promoter | ||||||
Function / homology | Initiator binding domain / Initiator binding protein 39kDa, C-terminal / IBP39, C-terminal domain superfamily / Transcription-initiator DNA-binding domain IBD / Initiator binding protein 39 kDa / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / 39 kDa initiator binding protein Function and homology information | ||||||
Biological species | Trichomonas vaginalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Schumacher, M.A. / Johnson, P.J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Structural Basis of Core Promoter Recognition in a Primitive Eukaryote Authors: Schumacher, M.A. / Lau, A.O.T. / Johnson, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q89.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q89.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 1q89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q89_validation.pdf.gz | 363.2 KB | Display | wwPDB validaton report |
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Full document | 1q89_full_validation.pdf.gz | 368.7 KB | Display | |
Data in XML | 1q89_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1q89_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/1q89 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/1q89 | HTTPS FTP |
-Related structure data
Related structure data | 1pp7C 1pp8C 1q87C 1q88SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 25727.221 Da / Num. of mol.: 1 / Fragment: C-domain, residues 127-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95VR4 |
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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: 2.08 Å3/Da / Density % sol: 40.92 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 5000, ammonium sulphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 10, 2001 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→76.5 Å / Num. obs: 6272 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.75→2.82 Å / % possible all: 89 |
Reflection | *PLUS % possible obs: 94 % / Num. measured all: 35034 |
Reflection shell | *PLUS Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Q88 Resolution: 2.75→76.5 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1178885.56 / 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: 32.2451 Å2 / ksol: 0.296272 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→76.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 76.5 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.198 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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