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Yorodumi- PDB-4cp1: Crystal Structure of Epithelial Adhesin 9 A domain (Epa9A) from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cp1 | |||||||||
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Title | Crystal Structure of Epithelial Adhesin 9 A domain (Epa9A) from Candida glabrata in complex with Galb1-3GlcNAc | |||||||||
Components | EPITHELIAL ADHESIN 9 | |||||||||
Keywords | CELL ADHESION / LECTIN / TISSUE INVASION / PATHOGENICITY | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | CANDIDA GLABRATA (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Kock, M. / Maestre-Reyna, M. / Diderrich, R. / Moesch, H.-U. / Essen, L.-O. | |||||||||
Citation | Journal: To Be Published Title: Functional reprogramming of Candida glabrata epithelial adhesins: the role of conserved and variable structural motifs in ligand binding Authors: Diderrich, R. / Kock, M. / Maestre-Reyna, M. / Rupp, S. / Essen, L.-O. / Moesch, H.-U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cp1.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cp1.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/4cp1 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/4cp1 | HTTPS FTP |
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-Related structure data
Related structure data | 4cp0C 4cp2C 4af9S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 33240.457 Da / Num. of mol.: 1 / Fragment: ADHESION DOMAIN (A DOMAIN), RESIDUES 39-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANDIDA GLABRATA (fungus) / Strain: CBS 138 / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): SHUFFLE T7 EXPRESS (C3029) / References: UniProt: B4UMX2 | ||||
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#2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.27 Å3/Da / Density % sol: 45.85 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop Details: 0.1 M HEPES PH7, 32% PEG 6000, 0.05 M LACTOSE, VAPOR DIFFUSION IN SITTING DROP, SOAKED WITH GALB1-3GLCNAC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARRESEARCH MARMOSAIC 255 MM / Detector: CCD / Date: Nov 16, 2012 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→41.21 Å / Num. obs: 10922 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PRUNED VERSION OF PDB ENTRY 4AF9 Resolution: 2.5→33.35 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 12.943 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED, PART OF LOOP L1 NOT DEFINED IN ELECTRON DENSITY, LYS A 76 - GLN A 108
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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: 21.827 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→33.35 Å
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Refine LS restraints |
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