+Open data
-Basic information
Entry | Database: PDB / ID: 4aj9 | ||||||
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Title | Catalase 3 from Neurospora crassa | ||||||
Components | CATALASE-3 | ||||||
Keywords | OXIDOREDUCTASE / 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: 1.85 Å | ||||||
Authors | Zarate-Romero, A. / Rudino-Pinera, E. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2019 Title: X-ray driven reduction of Cpd I of Catalase-3 from N. crassa reveals differential sensitivity of active sites and formation of ferrous state. Authors: Zarate-Romero, A. / Stojanoff, V. / Cohen, A.E. / 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 "BC" 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 "CA" 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 | 4aj9.cif.gz | 586.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aj9.ent.gz | 479.9 KB | Display | PDB format |
PDBx/mmJSON format | 4aj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/4aj9 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/4aj9 | HTTPS FTP |
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-Related structure data
Related structure data | 6nswC 6nsyC 6nszC 6nt0C 6nt1C 3ej6S 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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-Components
#1: Protein | Mass: 75642.211 Da / Num. of mol.: 4 / Fragment: RESIDUES 38-719 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Strain: 74-ORS23-1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C169, catalase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-1PE / #5: 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: 2.6 Å3/Da / Density % sol: 52.69 % / Description: NONE |
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Crystal grow | pH: 6.6 Details: 0.1 M MES PH 6.6, 20 % PEG 3350, 0.2 M AMMONIUM TARTRATE DIBASIC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 8, 2011 Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 269226 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.56 % / Biso Wilson estimate: 10.08 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.56 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.3 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EJ6 Resolution: 1.85→29.7 Å / SU ML: 0.47 / σ(F): 0.24 / Phase error: 20.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.441 Å2 / ksol: 0.388 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.7 Å
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Refine LS restraints |
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LS refinement shell |
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