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- PDB-1nml: Di-haemic Cytochrome c Peroxidase from Pseudomonas nautica 617, f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nml | |||||||||
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Title | Di-haemic Cytochrome c Peroxidase from Pseudomonas nautica 617, form IN (pH 4.0) | |||||||||
![]() | di-haem cytochrome c peroxidase | |||||||||
![]() | OXIDOREDUCTASE / PEROXIDASE / DI-HAEM / ELECTRON TRANSPORT | |||||||||
Function / homology | ![]() cytochrome-c peroxidase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dias, J.M. / Bonifacio, C. / Alves, T. / Pereira, A.S. / Bourgeois, D. / Moura, I. / Romao, M.J. | |||||||||
![]() | ![]() Title: Structural basis for the mechanism of Ca(2+) activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617 Authors: Dias, J.M. / Alves, T. / Pereira, A.S. / Bourgeois, D. / Moura, I. #1: ![]() Title: Crystallization and preliminary X-ray diffraction analysis of two-dependent forms of a di-haem cytochrome c peroxidase from Pseudomonas nautica Authors: Dias, J.M. / Bonifacio, C. / Alves, T. / Moura, J.J.G. / Moura, I. / Romao, M.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.5 KB | Display | ![]() |
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PDB format | ![]() | 64 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rz5C ![]() 1rz6C ![]() 1eb7S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35383.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: synonym Marinobacter hydrocarbonoclasticus Source: (natural) ![]() Strain: 617 / References: UniProt: P83787, cytochrome-c peroxidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-CIT / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.26 Å3/Da / Density % sol: 70.9 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 4 Details: sodium citrate, pH 4.0, VAPOR DIFFUSION, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Dias, J.M., (2002) Acta Cryst., D58, 697. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 18, 2000 |
Radiation | Monochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 35161 / Num. obs: 35072 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 45.6 Å2 / Rsym value: 0.055 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4 / Num. unique all: 3475 / Rsym value: 0.535 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 35359 / Num. measured all: 494949 / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 7.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EB7 Resolution: 2.2→20 Å / Cross valid method: Rfree / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 33291 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.45 |