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Yorodumi- PDB-1zbo: X-Ray Crystal Structure of Protein BPP1347 from Bordetella parape... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zbo | ||||||
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Title | X-Ray Crystal Structure of Protein BPP1347 from Bordetella parapertussis. Northeast Structural Genomics Consortium Target BoR27. | ||||||
Components | hypothetical protein BPP1347 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information LON domain-like fold / BPP1347 like domain / LON domain-like / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / Roll / Orthogonal Bundle ...LON domain-like fold / BPP1347 like domain / LON domain-like / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Bordetella parapertussis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Forouhar, F. / Yong, W. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Hypothetical Protein BPP1347 from Bordetella parapertussis, Northeast Structural Genomics Target BoR27. Authors: Forouhar, F. / Yong, W. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zbo.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zbo.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 1zbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zbo_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 1zbo_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 1zbo_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 1zbo_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/1zbo ftp://data.pdbj.org/pub/pdb/validation_reports/zb/1zbo | 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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Unit cell |
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-Components
#1: Protein | Mass: 23609.406 Da / Num. of mol.: 2 / Fragment: BPP1347 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella parapertussis (bacteria) / Strain: 12822 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7WAM7 #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: 2.44 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 180 mM sodium formate, 18% PEG3350, 5 mM DTT. , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97894 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97894 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 25814 / Num. obs: 25763 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.1 / Net I/σ(I): 26.15 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 8.5 / Num. unique all: 2561 / Rsym value: 0.468 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→29.53 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 273422.86 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.4944 Å2 / ksol: 0.277895 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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