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Yorodumi- PDB-2xg5: E. coli P pilus chaperone-subunit complex PapD-PapH bound to pilu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xg5 | ||||||
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Title | E. coli P pilus chaperone-subunit complex PapD-PapH bound to pilus biogenesis inhibitor, pilicide 5d | ||||||
Components |
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Keywords | CHAPERONE / CHAPERONE-SURFACE ACTIVE PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information cell adhesion involved in single-species biofilm formation / pilus / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space / extracellular region Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Remaut, H. / Phan, G. / Buelens, F. / Chorell, E. / Pinkner, J.S. / Edvinsson, S. / Almqvist, F. / Hultgren, S.J. / Waksman, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Design and Synthesis of C-2 Substituted Thiazolo and Dihydrothiazolo Ring-Fused 2-Pyridones: Pilicides with Increased Antivirulence Activity. Authors: Chorell, E. / Pinkner, J.S. / Phan, G. / Edvinsson, S. / Buelens, F. / Remaut, H. / Waksman, G. / Hultgren, S.J. / Almqvist, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xg5.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xg5.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xg5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2xg5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2xg5_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 2xg5_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xg5 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xg5 | HTTPS FTP |
-Related structure data
Related structure data | 2xg4C 2j2zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 24589.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-TERMINAL 6XHIS TAG / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P15319 |
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#2: Protein | Mass: 19297.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-TERMINAL RESIDUES 1-22 DELETED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P07111 |
-Non-polymers , 6 types, 207 molecules
#3: Chemical | ChemComp-GOL / |
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#4: Chemical | ChemComp-EC2 / ( |
#5: Chemical | ChemComp-EC5 / ( |
#6: Chemical | ChemComp-PGO / |
#7: Chemical | ChemComp-CO / |
#8: Water | ChemComp-HOH / |
-Details
Nonpolymer details | - (EC5): RADIOLYSIS |
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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: 3.7 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.01 M COBALT CHLORIDE, 0.1 M MES PH 6.5 AND 1.8 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 37302 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.8 |
Reflection shell | Highest resolution: 2 Å / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.5 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J2Z Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.909 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN ATOMS FOR WHICH NO DENSITY IS OBSERVED ARE MODELED WITH AS LIKELY CONFORMER AND WITH OCCUPANCY SET TO 0.01 ATOM RECORD. CONTAINS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN ATOMS FOR WHICH NO DENSITY IS OBSERVED ARE MODELED WITH AS LIKELY CONFORMER AND WITH OCCUPANCY SET TO 0.01 ATOM RECORD. CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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: 8.909 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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