+Open data
-Basic information
Entry | Database: PDB / ID: 5a29 | ||||||
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Title | Family 2 Pectate Lyase from Vibrio vulnificus | ||||||
Components |
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Keywords | LYASE / PECTIN / POLYSACCHARIDE LYASE / ENDOLYTIC / EXOLYTIC / BETA-ELIMINATION / ANCESTRAL GENE RESURRECTION / MAGNESIUM | ||||||
Function / homology | Function and homology information carbon-oxygen lyase activity, acting on polysaccharides / pectin catabolic process / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | VIBRIO VULNIFICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | McLean, R. / Hobbs, J.K. / Suits, M.D. / Tuomivaara, S. / Jones, D. / Boraston, A.B. / Abbott, D.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Functional Analyses of Resurrected and Contemporary Enzymes Illuminate an Evolutionary Path for the Emergence of Exolysis in Polysaccharide Lyase Family 2. Authors: Mclean, R. / Hobbs, J.K. / Suits, M.D. / Tuomivaara, S.T. / Jones, D. / Boraston, A.B. / Abbott, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a29.cif.gz | 142 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a29.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 5a29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/5a29 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/5a29 | HTTPS FTP |
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-Related structure data
Related structure data | 2v8jS S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 64677.500 Da / Num. of mol.: 1 / Fragment: RESIDUES 19-566 / Source method: isolated from a natural source / Source: (natural) VIBRIO VULNIFICUS (bacteria) / Strain: YJ016 / References: UniProt: Q7MCK3 |
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#2: Protein/peptide | Mass: 2036.202 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: CUSTOM SYNTHESIZED, CODON OPTIMIZED CODING SEQUENCE Source: (synth.) VIBRIO VULNIFICUS (bacteria) |
-Non-polymers , 4 types, 514 molecules
#3: Chemical | ChemComp-MN / | ||||
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#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Details
Sequence details | N-TERMINAL HISTIDINE AFFINITY TAG AND RESIDUES 18-556 ONLY. |
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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: 3.2 Å3/Da / Density % sol: 61.6 % / Description: NONE |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS OF VVPL2 DEVELOPED VIA HANGING DROP VAPOUR DIFFUSION METHOD AT A PROTEIN CONCENTRATION OF 15 MG/ML BY MIXING EQUAL AMOUNTS OF THE PROTEIN SOLUTION WITH A MOTHER LIQUOR CONSISTING OF ...Details: CRYSTALS OF VVPL2 DEVELOPED VIA HANGING DROP VAPOUR DIFFUSION METHOD AT A PROTEIN CONCENTRATION OF 15 MG/ML BY MIXING EQUAL AMOUNTS OF THE PROTEIN SOLUTION WITH A MOTHER LIQUOR CONSISTING OF 16% (W/V) POLYETHYLENE GLYCOL 3,350, 0.14 M NA/K TARTRATE, AND 0.1 M HEPES (PH 7.0) AT 19 DEGREES CELSIUS. CRYSTALS WERE CRYOPROTECTED BY BRIEF CRYSTAL IMMERSION INTO A SOLUTION OF THE RESERVOIR SOLUTION SUPPLEMENTED WITH 25% ETHYLENE GLYCOL, AND SUBSEQUENTLY FROZEN IN A LIQUID NITROGEN STREAM PRIOR TO DIFFRACTION EXPERIMENTS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2013 / Details: MIRRORS RH COATED |
Radiation | Monochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL SI(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→122 Å / Num. obs: 64624 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V8J Resolution: 1.9→122.2 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.439 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 0-17 THAT INCLUDE THE HISTIDINE-AFFINITY TAG, INTERDIGITATE FROM AN ADJACENT PROTEIN MOLECULE
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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: 27.831 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→122.2 Å
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Refine LS restraints |
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