+Open data
-Basic information
Entry | Database: PDB / ID: 7a1a | ||||||
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Title | 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus oryzae | ||||||
Components | Amidohydrolase 2 | ||||||
Keywords | METAL BINDING PROTEIN | ||||||
Function / homology | Function and homology information o-pyrocatechuate decarboxylase / o-pyrocatechuate decarboxylase activity / benzoate catabolic process via hydroxylation / secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / cytosol Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Hofer, G. / Keller, W. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Chembiochem / Year: 2021 Title: Metal Ion Promiscuity and Structure of 2,3-Dihydroxybenzoic Acid Decarboxylase of Aspergillus oryzae. Authors: Hofer, G. / Sheng, X. / Braeuer, S. / Payer, S.E. / Plasch, K. / Goessler, W. / Faber, K. / Keller, W. / Himo, F. / Glueck, S.M. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a1a.cif.gz | 425.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a1a.ent.gz | 339.5 KB | Display | PDB format |
PDBx/mmJSON format | 7a1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a1a_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7a1a_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7a1a_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 7a1a_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/7a1a ftp://data.pdbj.org/pub/pdb/validation_reports/a1/7a1a | HTTPS FTP |
-Related structure data
Related structure data | 7a19C 2dvtS 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: 41077.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: OAory_01010140 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S9DW14, UniProt: P80402*PLUS #2: Chemical | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.96 Å3/Da / Density % sol: 37.28 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M calcium acetate, 0.1M sodium acetate 4.5, 10% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→49.95 Å / Num. obs: 98740 / % possible obs: 99.64 % / Redundancy: 23.7 % / Biso Wilson estimate: 15.44 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.2276 / Rpim(I) all: 0.05 / Rrim(I) all: 0.2332 / Net I/σ(I): 8.94 |
Reflection shell | Resolution: 1.53→1.584 Å / Redundancy: 24.5 % / Rmerge(I) obs: 0.8963 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 9747 / CC1/2: 0.959 / CC star: 0.989 / % possible all: 99.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DVT Resolution: 1.53→49.95 Å / SU ML: 0.1772 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.8959 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→49.95 Å
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Refine LS restraints |
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LS refinement shell |
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