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Yorodumi- PDB-4ahz: Flo5A showing a heptanuclear gadolinium cluster on its surface af... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ahz | ||||||
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Title | Flo5A showing a heptanuclear gadolinium cluster on its surface after 60 min of soaking | ||||||
Components | FLOCCULATION PROTEIN FLO5 | ||||||
Keywords | CELL ADHESION / ADHESIN / FLOCCULIN | ||||||
Function / homology | Function and homology information flocculation / fungal-type cell wall / cell-substrate adhesion / D-mannose binding / side of membrane / cell periphery / extracellular region Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Veelders, M. / Essen, L.-O. | ||||||
Citation | Journal: Chembiochem / Year: 2012 Title: Complex Gadolinium-Oxo Clusters Formed Along Concave Protein Surfaces. Authors: Veelders, M. / Essen, L.-O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ahz.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ahz.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ahz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ahz_validation.pdf.gz | 427.9 KB | Display | wwPDB validaton report |
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Full document | 4ahz_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | 4ahz_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 4ahz_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/4ahz ftp://data.pdbj.org/pub/pdb/validation_reports/ah/4ahz | HTTPS FTP |
-Related structure data
Related structure data | 4ahwC 4ahxC 4ahyC 4ai0C 4ai1C 4ai2C 4ai3C 2xjpS 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
#1: Protein | Mass: 29097.939 Da / Num. of mol.: 1 / Fragment: LECTIN-LIKE DOMAIN, RESIDUES 23-271 Source method: isolated from a genetically manipulated source Details: SOAKED 90 MIN WITH GDAC3 Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): ORIGAMI 2 / References: UniProt: P38894 | ||||||
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#2: Chemical | ChemComp-GD / #3: Chemical | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.41 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 200 MM BISTRIS PROPANE, 500 MM NACL, 3 MM GDAC3, 20% PEG 4000, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 2, 2009 / Details: BENT CYLINDRICAL MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.27 Å / Num. obs: 24900 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2XJP Resolution: 1.9→19.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.919 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 197 - 199 ARE NOT WELL DEFINED. RESIDUES 199 - 204 HAVE BEEN MODELLED IN TWO DISTINCT CONFORMATION
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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: 21.143 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.17 Å
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Refine LS restraints |
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