+Open data
-Basic information
Entry | Database: PDB / ID: 1eb6 | ||||||
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Title | Deuterolysin from Aspergillus oryzae | ||||||
Components | NEUTRAL PROTEASE II | ||||||
Keywords | HYDROLASE / METALLOPROTEINASE / ZINC / NEUTRAL PROTEASE II | ||||||
Function / homology | Function and homology information deuterolysin / metalloendopeptidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ASPERGILLUS ORYZAE (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1 Å | ||||||
Authors | McAuley, K.E. / Jia-Xing, Y. / Dodson, E.J. / Lehmbeck, J. / Ostergaard, P.R. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: A Quick Solution: Ab Initio Structure Determination of a 19 kDa Metalloproteinase Using Acorn Authors: Mcauley, K.E. / Jia-Xing, Y. / Dodson, E.J. / Lehmbeck, J. / Ostergaard, P.R. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eb6.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eb6.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 1eb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eb6_validation.pdf.gz | 432 KB | Display | wwPDB validaton report |
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Full document | 1eb6_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 1eb6_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1eb6_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/1eb6 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/1eb6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19031.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ASPERGILLUS ORYZAE (mold) / References: UniProt: P46076, deuterolysin | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THERMOSTAB | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 1.8M NA,K PHOSPHATE, 0.1M HEPES PH 7.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1→30 Å / Num. obs: 82199 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1→1.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5 / % possible all: 99.8 |
Reflection shell | *PLUS % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 1→57.73 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.22 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.019 / 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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→57.73 Å
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Refine LS restraints |
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