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Yorodumi- PDB-3zj5: NEUROSPORA CRASSA CATALASE-3 EXPRESSED IN E. COLI, ORTHORHOMBIC FORM. -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zj5 | ||||||
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Title | NEUROSPORA CRASSA CATALASE-3 EXPRESSED IN E. COLI, ORTHORHOMBIC FORM. | ||||||
Components | CATALASE-3 | ||||||
Keywords | OXIDOREDUCTASE / HYDROGEN PEROXIDE / PEROXIDASE | ||||||
Function / homology | Function and homology information catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | NEUROSPORA CRASSA (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Zarate-Romero, A. / Rudino-Pinera, E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Conformational Stability and Crystal Packing: Polymorphism in Neurospora Crassa Cat-3 Authors: Zarate-Romero, A. / Stojanoff, V. / Rojas-Trejo, S.P. / Hansberg, W. / Rudino-Pinera, E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zj5.cif.gz | 590.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zj5.ent.gz | 482.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zj5_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3zj5_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3zj5_validation.xml.gz | 114 KB | Display | |
Data in CIF | 3zj5_validation.cif.gz | 169.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/3zj5 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/3zj5 | HTTPS FTP |
-Related structure data
Related structure data | 3zj4C 4bimC 3ej6S C: citing same article (ref.) 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 , 1 types, 4 molecules ABCD
#1: Protein | Mass: 82552.141 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: BEFORE RESIDUE 1 A HIS TAG SIGNATURE IS PRESENT / Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9C169, catalase |
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-Non-polymers , 6 types, 2220 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PG4 / #4: Chemical | #5: Chemical | ChemComp-HEM / #6: Chemical | ChemComp-TAR / | #7: 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: 2.63 Å3/Da / Density % sol: 53.18 % / Description: NONE |
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Crystal grow | pH: 6.6 Details: 200 MM AMMONIUM DIBASIC TARTRATE, 20 % PEG 3350, pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9794 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2012 Details: SI(111) CHANNEL CUT MONOCHROMATOR, TOROIDAL FOCUSING MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→42.5 Å / Num. obs: 270245 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EJ6 Resolution: 1.95→42.525 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 17.76 / Stereochemistry target values: ML
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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: 11.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→42.525 Å
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Refine LS restraints |
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LS refinement shell |
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