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Yorodumi- PDB-5eb4: The crystal structure of almond HNL, PaHNL5 V317A, expressed in A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eb4 | |||||||||
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Title | The crystal structure of almond HNL, PaHNL5 V317A, expressed in Aspergillus niger | |||||||||
Components | Hnl isoenzyme 5 | |||||||||
Keywords | LYASE / hydroxynitrile lyase / Prunus amygdalus / Aspergillus niger | |||||||||
Function / homology | Function and homology information mandelonitrile lyase activity / (R)-mandelonitrile lyase / oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding Similarity search - Function | |||||||||
Biological species | Prunus dulcis (almond) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Pavkov-Keller, T. / Steinkellner, G. / Gruber, K. | |||||||||
Funding support | Austria, 1items
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Citation | Journal: J.Biotechnol. / Year: 2016 Title: Structures of almond hydroxynitrile lyase isoenzyme 5 provide a rationale for the lack of oxidoreductase activity in flavin dependent HNLs. Authors: Pavkov-Keller, T. / Bakhuis, J. / Steinkellner, G. / Jolink, F. / Keijmel, E. / Birner-Gruenberger, R. / Gruber, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eb4.cif.gz | 225.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eb4.ent.gz | 178.8 KB | Display | PDB format |
PDBx/mmJSON format | 5eb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/5eb4 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/5eb4 | HTTPS FTP |
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-Related structure data
Related structure data | 5eb5C 1ju2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 57903.172 Da / Num. of mol.: 2 / Fragment: UNP residues 28-559 / Mutation: V317A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prunus dulcis (almond) / Gene: hnl5 / Production host: Aspergillus niger (mold) / References: UniProt: Q7XJE8, UniProt: O24243*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: The initial protein concentration was 28 mg/ml (10mM L-Malic acid, MES, Tris pH 7). Different crystal forms were obtained under crystallization conditions varying - PEG 4K, isopropanol and ...Details: The initial protein concentration was 28 mg/ml (10mM L-Malic acid, MES, Tris pH 7). Different crystal forms were obtained under crystallization conditions varying - PEG 4K, isopropanol and 10mM Hepes pH 7-7.8 with protein concentration 19-28 mg/ml. Most of the crystals that appeared within 2 weeks had visual grow defects. In one of the drops the stack of thin plates appeared after 1 month and one complete dataset was collected. PH range: 7.0 - 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: data were collected at the microfocus beamline (SLS) in 3 passes, since the automatic centering of the small thin, plate-like crystal was difficult |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.1 Å / Num. obs: 49502 / % possible obs: 91.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.5 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ju2 Resolution: 2.3→49.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.043 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 25.658 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→49.09 Å
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Refine LS restraints |
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