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Yorodumi- PDB-4jeb: Crystal structure of an engineered RIDC1 tetramer with four inter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jeb | ||||||
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Title | Crystal structure of an engineered RIDC1 tetramer with four interfacial disulfide bonds and four three-coordinate Zn(II) sites | ||||||
Components | soluble cytochrome b562 | ||||||
Keywords | ELECTRON TRANSPORT / four-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 / Resolution: 2.3 Å | ||||||
Authors | Tezcan, F.A. / Medina-Morales, A.M. / Perez, A. / Brodin, J.D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: In Vitro and Cellular Self-Assembly of a Zn-Binding Protein Cryptand via Templated Disulfide Bonds. Authors: Medina-Morales, A. / Perez, A. / Brodin, J.D. / 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 | 4jeb.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jeb.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jeb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4jeb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4jeb_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 4jeb_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/4jeb ftp://data.pdbj.org/pub/pdb/validation_reports/je/4jeb | HTTPS FTP |
-Related structure data
Related structure data | 4je9C 4jeaC 3iq6S 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 11564.073 Da / Num. of mol.: 2 / Fragment: UNP residues 23-128 Mutation: R34A, L38A, Q41W, K42S, K59A, D66W, V69I, D73H, D74A, K77H, E81C, T96C, 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) / Strain (production host): B21(DE3) / References: UniProt: P0ABE7 #2: Chemical | #3: Chemical | #4: 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: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 35% methyl-pentandiol, 0.1M HEPES pH 7.5, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 30, 2012 / Details: K-B focusing mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.158→48.553 Å / Num. all: 13468 / Num. obs: 13468 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rsym value: 0.094 / Net I/σ(I): 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IQ6 Resolution: 2.3→48.55 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.207 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.298 / 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: 89.55 Å2 / Biso mean: 57.6607 Å2 / Biso min: 26.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 839 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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