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Open data
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Basic information
Entry | Database: PDB / ID: 6rpe | ||||||
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Title | Structure of 5% reduced KpDyP in complex with cyanide | ||||||
![]() | Iron-dependent peroxidase | ||||||
![]() | OXIDOREDUCTASE / heme protein | ||||||
Function / homology | ![]() Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pfanzagl, V. / Beale, J. / Hofbauer, S. | ||||||
![]() | ![]() Title: X-ray-induced photoreduction of heme metal centers rapidly induces active-site perturbations in a protein-independent manner. Authors: Pfanzagl, V. / Beale, J.H. / Michlits, H. / Schmidt, D. / Gabler, T. / Obinger, C. / Djinovic-Carugo, K. / Hofbauer, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 461 KB | Display | ![]() |
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PDB format | ![]() | 376.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 51.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rpdC ![]() 6rqyC ![]() 6rr1C ![]() 6rr4C ![]() 6rr5C ![]() 6rr6C ![]() 6rr8C ![]() 6fksS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33453.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: yfeX, AGG09_21550, B1727_13990, B8011_07420, BL102_0001560, BN49_3985, BVX91_12125, CEO55_07245, CIT28_09840, CP905_14695, PMK1_00271, SAMEA3531778_01640, SM57_03027 Production host: ![]() ![]() References: UniProt: A0A0W8ATM9, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases |
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-Non-polymers , 5 types, 793 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 23% w/v PEG 3350, 0.1 M MgCl2, 0.1 M Tris-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.991874 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→36.31 Å / Num. obs: 51235 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 10.69 Å2 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.8→1.81 Å / Num. unique obs: 3003 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FKS Resolution: 1.8→36.31 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.12
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Displacement parameters | Biso mean: 10.34 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→36.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.81 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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