+Open data
-Basic information
Entry | Database: PDB / ID: 2p9j | ||||||
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Title | Crystal structure of AQ2171 from Aquifex aeolicus | ||||||
Components | Hypothetical protein AQ2171 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / AQ2171 / SECSG / RIKEN / PSI / Aquifex aeolicus / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Yang, H. / Chen, L. / Agari, Y. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of AQ2171 from Aquifex aeolicus Authors: Yang, H. / Chen, L. / Agari, Y. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Rose, J.P. / 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 | 2p9j.cif.gz | 242.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p9j.ent.gz | 206.4 KB | Display | PDB format |
PDBx/mmJSON format | 2p9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p9j_validation.pdf.gz | 479.8 KB | Display | wwPDB validaton report |
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Full document | 2p9j_full_validation.pdf.gz | 494.6 KB | Display | |
Data in XML | 2p9j_validation.xml.gz | 45.4 KB | Display | |
Data in CIF | 2p9j_validation.cif.gz | 63.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/2p9j ftp://data.pdbj.org/pub/pdb/validation_reports/p9/2p9j | 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
#1: Protein | Mass: 18394.002 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_2171 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: O67920 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.39 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 4.69 Details: 25% w/v PEG 4000, 0.1 M Na Acetate, Acetic acid pH 4.69, 0.2M Ammonium Acetate, MICROBATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97930, 0.90000, 0.97945 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 2006 | ||||||||||||
Radiation | Monochromator: SI CHANNEL 220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→33.92 Å / Num. obs: 49520 / Redundancy: 7.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 25.2 | ||||||||||||
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 4.39 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→33.92 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.87 / SU B: 9.935 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.751 / ESU R Free: 0.308 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→33.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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