+Open data
-Basic information
Entry | Database: PDB / ID: 3k4p | ||||||
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Title | Aspergillus niger Phytase | ||||||
Components | 3-phytase A | ||||||
Keywords | HYDROLASE / Phytase / PhyA / 3-Phosphotase / myo-inositol hexakis phosphate phosphohydrolase / 37288-11-2 / Disulfide bond / Glycoprotein / Secreted | ||||||
Function / homology | Function and homology information 3-phytase / 3-phytase activity / acid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Oakley, A.J. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2010 Title: The structure of Aspergillus niger phytase PhyA in complex with a phytate mimetic Authors: Oakley, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k4p.cif.gz | 185.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k4p.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 3k4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k4p_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 3k4p_full_validation.pdf.gz | 476.1 KB | Display | |
Data in XML | 3k4p_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 3k4p_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/3k4p ftp://data.pdbj.org/pub/pdb/validation_reports/k4/3k4p | HTTPS FTP |
-Related structure data
Related structure data | 3k4qC 1ihpS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 7 - 444 / Label seq-ID: 7 - 444
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-Components
#1: Protein | Mass: 48888.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Gene: phyA / Production host: Aspergillus niger (mold) / References: UniProt: P34752, 3-phytase #2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% (w/v) PEG 3350, 0.4M ammonium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953715 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2009 / Details: BEAMLINE OPTICS |
Radiation | Monochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953715 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→76.74 Å / Num. all: 35613 / Num. obs: 35613 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5338 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IHP Resolution: 2.4→66.36 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.873 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.744 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / ESU R: 0.635 / ESU R Free: 0.314 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.71 Å2 / Biso mean: 26.967 Å2 / Biso min: 2.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→66.36 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3363 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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