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Yorodumi- PDB-2fqp: Crystal structure of a cupin domain (bp2299) from bordetella pert... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fqp | ||||||
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Title | Crystal structure of a cupin domain (bp2299) from bordetella pertussis tohama i at 1.80 A resolution | ||||||
Components | hypothetical protein BP2299 | ||||||
Keywords | METAL BINDING PROTEIN / Double-stranded beta-helix fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bordetella pertussis Tohama I (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of (np_880937.1) from BORDETELLA PERTUSSIS at 1.80 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV ROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fqp.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fqp.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fqp_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 2fqp_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 2fqp_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 2fqp_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/2fqp ftp://data.pdbj.org/pub/pdb/validation_reports/fq/2fqp | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / Refine code: 5
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-Components
#1: Protein | Mass: 10927.838 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria) Species: Bordetella pertussis / Strain: Tohama I / Gene: np_880937.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / References: GenBank: 33593293, UniProt: Q7VWF8*PLUS #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-1PE / | #5: 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: 1.83 Å3/Da / Density % sol: 36.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5 Details: 0.2M NaOAc, 30.0% PEG-4000, 0.1M TRIS pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.019867, 0.979741 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 11, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→19 Å / Num. obs: 27712 / % possible obs: 90.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 13.16 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.746 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.136 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THERE IS A METAL ION BOUND IN EACH MONOMER. IT IS ASSIGNED AS ZN2+ BASED ON AN X-RAY EMISSION SPECTRUM AND AN X-RAY FLUORESCENCE ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THERE IS A METAL ION BOUND IN EACH MONOMER. IT IS ASSIGNED AS ZN2+ BASED ON AN X-RAY EMISSION SPECTRUM AND AN X-RAY FLUORESCENCE SCAN NEAR ZN ABSORPTION EDGE. (3) THERE IS AN ACETATE ION IN EACH MONOMER BOUND NEAR ZN2+ ION. (4) THERE IS A PENTAETHYLENE GLYCOL 238 (N=5) MOLECULE BOUND IN THE STRUCTURE. THE SOURCE OF PENTAETHYLENE GLYCOL IS UNCERTAIN. IT MAY COME FROM THE CONTAMINATION OF PEG400 USED IN THE EXPERIMENT. IT IS ALSO POSSIBLE THAT WE ONLY OBSERVE THE ORDERED PART OF PEG400 AND THE REST OF PEG400 IS DISORDERED. (5) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.089 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.847 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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