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- PDB-2bh4: X-ray structure of the M100K variant of ferric cyt c-550 from Par... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bh4 | ||||||
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Title | X-ray structure of the M100K variant of ferric cyt c-550 from Paracoccus versutus determined at 100 K. | ||||||
![]() | CYTOCHROME C-550 | ||||||
![]() | ELECTRON TRANSFER / C-TYPE CYTOCHROME / HEME / AXIAL LIGAND / PYRROLIDONE CARBOXYLIC ACID | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Worrall, J.A.R. / Van Roon, A.-M.M. / Ubbink, M. / Canters, G.W. | ||||||
![]() | ![]() Title: The Effect of Replacing the Axial Methionine Ligand with a Lysine Residue in Cytochrome C-550 from Paracoccus Versutus Assessed by X-Ray Crystallography and Unfolding. Authors: Worrall, J.A.R. / Van Roon, A.-M.M. / Ubbink, M. / Canters, G.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.4 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798.3 KB | Display | ![]() |
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Full document | ![]() | 799.8 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 14154.857 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-HEC / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | WILD-TYPE GENE ACCESSION NUMBER | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37 % Description: STRUCTURE WAS ALREADY SOLVED FOR A CRYSTAL MEASURED AT 295 K. |
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Crystal grow | pH: 9 / Details: 3.2 M AMMONIUM SULFATE, 0.1 M BICINE PH9, pH 9.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 28, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→43.85 Å / Num. obs: 17450 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 11.7 / % possible all: 82.6 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.55→43.85 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1 AND 122-134 ARE NOT OBSERVED. RESIDUES 97-101 ARE MODELED IN A DOUBLE MAIN-CHAIN CONFORMATION.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→43.85 Å
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Refine LS restraints |
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