+Open data
-Basic information
Entry | Database: PDB / ID: 4ahy | ||||||
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Title | Flo5A cocrystallized with 3 mM GdAc3 | ||||||
Components | FLOCCULATION PROTEIN FLO5 | ||||||
Keywords | SUGAR BINDING PROTEIN / GADOLINIUM / CLUSTER / ADHESIN | ||||||
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 S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 4ahy.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ahy.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ahy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/4ahy ftp://data.pdbj.org/pub/pdb/validation_reports/ah/4ahy | HTTPS FTP |
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-Related structure data
Related structure data | 4ahwC 4ahxC 4ahzC 4ai0C 4ai1C 4ai2C 4ai3C 2xjpS 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
#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 Source: (gene. exp.) SACCHAROMYCES CEREVISIAE S288C (yeast) / 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 / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 200 MM BISTRIS PROPANE, 500 MM NACL, 3 MM GDAC3, 20% PEG4000, 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: Feb 25, 2009 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→19.37 Å / Num. obs: 43091 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.8 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XJP Resolution: 1.7→19.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.308 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 18.758 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.29 Å
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Refine LS restraints |
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