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Yorodumi- PDB-2x3b: AsaP1 inactive mutant E294A, an extracellular toxic zinc metalloe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x3b | ||||||
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Title | AsaP1 inactive mutant E294A, an extracellular toxic zinc metalloendopeptidase | ||||||
Components | TOXIC EXTRACELLULAR ENDOPEPTIDASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | AEROMONAS SALMONICIDA SUBSP. ACHROMOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Bogdanovic, X. / Palm, G.J. / Singh, R.K. / Hinrichs, W. | ||||||
Citation | Journal: FEBS Lett. / Year: 2016 Title: Structural Evidence of Intramolecular Propeptide Inhibition of the Aspzincin Metalloendopeptidase Asap1. Authors: Bogdanovic, X. / Palm, G.J. / Schwenteit, J. / Singh, R.K. / Gudmundsdottir, B.K. / Hinrichs, W. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Asap1_E294A and Asap1_E294Q, Two Inactive Mutants of the Toxic Zinc Metallopeptidase Asap1 from Aeromonas Salmonicida Subsp. Achromogenes. Authors: Bogdanovic, X. / Singh, R.K. / Hentschke, J. / Gudmundsdottir, B.K. / Hinrichs, W. #2: Journal: J.Bacteriol. / Year: 2009 Title: The Asap1 Peptidase of Aeromonas Salmonicida Subsp. Achromogenes is a Highly Conserved Deuterolysin Metalloprotease (Family M35) and a Major Virulence Factor. Authors: Arnadottir, H. / Hvanndal, I. / Andresdottir, V. / Burr, S.E. / Frey, J. / Gudmundsdottir, B.K. #3: Journal: Dis.Aquat.Organ. / Year: 1990 Title: Isolation of a New Toxic Protease from a Strain of Aeromonas Salmonicida Subspecies Achromogenes Authors: Gudmundsdottir, B.K. / Hastingst, S. / Ellis, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x3b.cif.gz | 187.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x3b.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3b ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3b | HTTPS FTP |
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-Related structure data
Related structure data | 2x3aC 2x3cSC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.0827, -0.99246, -0.09045), Vector: |
-Components
#1: Protein | Mass: 37228.488 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) AEROMONAS SALMONICIDA SUBSP. ACHROMOGENES (bacteria) Strain: KELDUR265-87 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PRI3715 / References: UniProt: Q8GMV9, deuterolysin #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.16 Å3/Da / Density % sol: 43.06 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 15% PEG 4000, 0.2 M (NH2)4SO4, 0.1 M HEPES PH 7.5, 10% ISO-PROPANOL |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97784 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 26, 2009 / Details: MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97784 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→90 Å / Num. obs: 33551 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.69 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X3C Resolution: 2.28→91.81 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.878 / SU B: 10.693 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.28 / 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 mean: 34.358 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→91.81 Å
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