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Yorodumi- PDB-2nr7: Structural Genomics, the crystal structure of putative secretion ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nr7 | ||||||
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Title | Structural Genomics, the crystal structure of putative secretion activator protein from Porphyromonas gingivalis W83 | ||||||
Components | Secretion activator protein, putative | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APCC85792 / Secretion activator / Porphyromonas gingivalis W83 / PSI-2 / Protein structure initiative / MCSG / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information TtsA-like, Glycoside hydrolase family 108 domain / Peptidoglycan binding domain / Glycosyl hydrolase 108 / Predicted Peptidoglycan domain / Chitosanase, subunit A; domain 1 / Chitosanase, subunit A, domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Lysozyme-like domain superfamily / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Porphyromonas gingivalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å | ||||||
Authors | Tan, K. / Bigelow, L. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of putative secretion activator protein from Porphyromonas gingivalis W83 Authors: Tan, K. / Bigelow, L. / Gu, M. / 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 | 2nr7.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nr7.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 2nr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/2nr7 ftp://data.pdbj.org/pub/pdb/validation_reports/nr/2nr7 | HTTPS FTP |
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-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: 22279.146 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Plasmid: pMCGS19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7MXB3 |
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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: 2.09 Å3/Da / Density % sol: 41.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Bis Tris pH5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2006 / Details: mirror |
Radiation | Monochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→26.93 Å / Num. all: 42196 / Num. obs: 42196 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 38 |
Reflection shell | Resolution: 1.3→1.31 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.92 / Num. unique all: 1024 / % possible all: 68.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.3→26.93 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.774 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.06 / 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: 19.437 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→26.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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