+Open data
-Basic information
Entry | Database: PDB / ID: 1r4v | ||||||
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Title | 1.9A crystal structure of protein AQ328 from Aquifex aeolicus | ||||||
Components | Hypothetical protein AQ_328 | ||||||
Keywords | Structural genomics / unknown function / all-alpha / histon fold / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Qiu, Y. / Tereshko, V. / Kim, Y. / Zhang, R. / Collart, F. / Joachimiak, A. / Kossiakoff, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proteins / Year: 2006 Title: The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold. Authors: Qiu, Y. / Tereshko, V. / Kim, Y. / Zhang, R. / Collart, F. / Yousef, M. / Kossiakoff, A. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r4v.cif.gz | 48 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r4v.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r4v_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
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Full document | 1r4v_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 1r4v_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1r4v_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r4v ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r4v | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20151.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: AQ_328 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O66665 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CAC / | #4: 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: 2.75 Å3/Da / Density % sol: 55.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 3350, sodium chloride, Zinc Acetate, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.95372, 0.97932, 0.97952 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Aug 23, 2003 / Details: mirrors | ||||||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 17815 / Num. obs: 17815 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.098 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.57 / Num. unique all: 948 / % possible all: 50.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.808 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.124 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.191 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.953 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: -0.8444 Å / Origin y: 16.3246 Å / Origin z: 12.8464 Å
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