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Yorodumi- PDB-1zx3: Structure of NE0241 Protein of Unknown Function from Nitrosomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zx3 | ||||||
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Title | Structure of NE0241 Protein of Unknown Function from Nitrosomonas europaea | ||||||
Components | hypothetical protein NE0241 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein NE0241 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | NE0241-like / Ribbon-helix-helix / Helix Hairpins / regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / : / Uncharacterized protein Function and homology information | ||||||
Biological species | Nitrosomonas europaea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Osipiuk, J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of hypothetical protein NE0241 from Nitrosomonas europaea. Authors: Osipiuk, J. / Cuff, M. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zx3.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zx3.ent.gz | 20.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zx3_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 1zx3_full_validation.pdf.gz | 434.4 KB | Display | |
Data in XML | 1zx3_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 1zx3_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/1zx3 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/1zx3 | 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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2 |
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3 |
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Unit cell |
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Details | the biological assembly is unknown |
-Components
#1: Protein | Mass: 14840.761 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: ATCC 19718 / Gene: NE0241 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: GenBank: 30248265, UniProt: Q82XL7*PLUS |
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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: 2.2 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M Bis-Tris, 1.4 M sodium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Apr 3, 2005 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 4689 / Num. obs: 4689 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 43.9 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 3.29 / Num. unique all: 363 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 21.76 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.419 / ESU R Free: 0.281 / 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: 47.733 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.497→2.562 Å / Total num. of bins used: 20
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