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Yorodumi- PDB-3nmk: Crystal structure of a zinc mediated dimer for the phenanthroline... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nmk | ||||||
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Title | Crystal structure of a zinc mediated dimer for the phenanthroline-modified cytochrome cb562 variant, MBP-Phen2 | ||||||
Components | Soluble cytochrome b562 | ||||||
Keywords | ELECTRON TRANSPORT / 4-helix-bundle | ||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Radford, R.J. / Tezcan, F.A. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2011 Title: Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites. Authors: Radford, R.J. / Lawrenz, M. / Nguyen, P.C. / McCammon, J.A. / Tezcan, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nmk.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nmk.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 3nmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nmk_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3nmk_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3nmk_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 3nmk_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/3nmk ftp://data.pdbj.org/pub/pdb/validation_reports/nm/3nmk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106
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-Components
#1: Protein | Mass: 11461.927 Da / Num. of mol.: 4 / Mutation: W59C, R62A, H63A, D66A, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-PXX / #4: Chemical | #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: 3.41 Å3/Da / Density % sol: 63.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris, 0.2 M ammonium sulfate, 30% PEG 400, 12.4 mM zinc chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→86.141 Å / Num. all: 15237 / Num. obs: 15237 / % possible obs: 100 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4 / Redundancy: 7.7 % / Rsym value: 0.113 / Net I/σ(I): 17.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 39.58 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→86.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.1971 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8215 / SU B: 11.963 / SU ML: 0.24 / SU R Cruickshank DPI: 2.0825 / SU Rfree: 0.3321 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.34 Å2 / Biso mean: 37.6472 Å2 / Biso min: 9.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→86.14 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 798 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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