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Yorodumi- PDB-2gz4: 1.5 A Crystal Structure of a Protein of Unknown Function ATU1052 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gz4 | ||||||
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Title | 1.5 A Crystal Structure of a Protein of Unknown Function ATU1052 from Agrobacterium tumefaciens | ||||||
Components | Hypothetical protein Atu1052 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Agrobacterium tumefaciens / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Hypothetical protein af1432 / Hypothetical protein af1432 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein / : Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: 1.5A crystal structure of a hypothetical protein Atu1052 from Agrobacterium tumefaciens Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gz4.cif.gz | 346.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gz4.ent.gz | 286.6 KB | Display | PDB format |
PDBx/mmJSON format | 2gz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gz4_validation.pdf.gz | 456.1 KB | Display | wwPDB validaton report |
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Full document | 2gz4_full_validation.pdf.gz | 466 KB | Display | |
Data in XML | 2gz4_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 2gz4_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/2gz4 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/2gz4 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The biological assembly is dimer. |
-Components
#1: Protein | Mass: 22906.484 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: GI:17934959 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UGI5, UniProt: Q7D028*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M NH4 Formate, 12% PEG3350, 4%MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→80.85 Å / Num. all: 123031 / Num. obs: 119242 / % possible obs: 96.92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.07 |
Reflection shell | Resolution: 1.5→1.538 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 2.1 / % possible all: 71.07 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→24.13 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.393 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.071 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.355 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→24.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.538 Å / Total num. of bins used: 20
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