+Open data
-Basic information
Entry | Database: PDB / ID: 4cp6 | ||||||
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Title | The Crystal structure of Pneumococcal vaccine antigen PcpA | ||||||
Components | CHOLINE BINDING PROTEIN PCPA | ||||||
Keywords | CHOLINE-BINDING PROTEIN / CHOLINE BINDING PROTEIN / LEUCINE-RICH REPEAT | ||||||
Function / homology | Function and homology information BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.34 Å | ||||||
Authors | Vallee, F. / Steier, V. / Oloo, E. / Chawla, D. / Vonrhein, C. / Steinmetz, A. / Mathieu, M. / Rak, A. / Mikol, V. / Oomen, R. | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of Pneumoccocal Vaccine Antigen Pcpa Authors: Vallee, F. / Steier, V. / Oloo, E. / Chawla, D. / Vonrhein, C. / Steinmetz, A. / Mathieu, M. / Rak, A. / Mikol, V. / Oomen, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cp6.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cp6.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/4cp6 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/4cp6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49500.129 Da / Num. of mol.: 1 / Fragment: CHOLINE-BINDING DOMAIN, RESIDUES 27-470 / Source method: isolated from a natural source / Source: (natural) STREPTOCOCCUS PNEUMONIAE (bacteria) / References: UniProt: Q97NB5, UniProt: A0A0H2USF9*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: 2.31 Å3/Da / Density % sol: 46.79 % / Description: USE PLATINIUM K2PTCL4 AS HEAVY ATOM DERIVATIVE |
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Crystal grow | pH: 4.6 / Details: pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9395 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→19.2 Å / Num. obs: 103647 / % possible obs: 98.5 % / Observed criterion σ(I): 1.7 / Redundancy: 6.2 % / Biso Wilson estimate: 15.04 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.34→1.36 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.7 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 1.34→19.2 Å / Cor.coef. Fo:Fc: 0.9565 / Cor.coef. Fo:Fc free: 0.9499 / SU R Cruickshank DPI: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.053 / SU Rfree Blow DPI: 0.052 / SU Rfree Cruickshank DPI: 0.049 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 19.57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.151 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→19.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.34→1.38 Å / Total num. of bins used: 20
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