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Yorodumi- PDB-3kq5: Crystal structure of an uncharacterized protein from Coxiella burnetii -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kq5 | ||||||
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Title | Crystal structure of an uncharacterized protein from Coxiella burnetii | ||||||
Components | Hypothetical cytosolic protein | ||||||
Keywords | Structural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Hypothetical protein af1432 - #40 / Putative conjugal transfer nickase/helicase TraI, C-terminal / Putative conjugal transfer nickase/helicase TraI C-term / Hypothetical protein af1432 / Winged helix DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Hypothetical cytosolic protein Function and homology information | ||||||
Biological species | Coxiella burnetii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Bonanno, J.B. / Freeman, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an uncharacterized protein from Coxiella burnetii Authors: Bonanno, J.B. / Freeman, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kq5.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kq5.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kq5_validation.pdf.gz | 424 KB | Display | wwPDB validaton report |
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Full document | 3kq5_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 3kq5_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 3kq5_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/3kq5 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/3kq5 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
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: 44473.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: CBU_0560 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83DY0 |
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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: 2.17 Å3/Da / Density % sol: 43.4 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.5 Details: 100mM Bis-Tris pH 6.5, 28% PEG 3350, 200mM ammonium acetate, vapor diffusion, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.245 Å / Num. all: 26838 / Num. obs: 25952 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3723 / Rsym value: 0.452 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.843 / SU B: 9.766 / SU ML: 0.122 / SU R Cruickshank DPI: 0.187 / SU Rfree: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.157 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.3 Å2 / Biso mean: 24.138 Å2 / Biso min: 3.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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