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Yorodumi- PDB-4je9: Crystal structure of an engineered metal-free RIDC1 construct wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4je9 | ||||||
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Title | Crystal structure of an engineered metal-free RIDC1 construct with four interfacial disulfide bonds | ||||||
Components | Soluble cytochrome b562 | ||||||
Keywords | ELECTRON TRANSPORT / four-helix bundle | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 | 4je9.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4je9.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 4je9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/4je9 ftp://data.pdbj.org/pub/pdb/validation_reports/je/4je9 | HTTPS FTP |
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-Related structure data
Related structure data | 4jeaC 4jebC 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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 11675.152 Da / Num. of mol.: 2 / Fragment: UNP residues 23-128 Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, 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): BL21(DE3) / References: UniProt: P0ABE7 #2: Chemical | #3: 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: 2.54 Å3/Da / Density % sol: 51.48 % |
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Crystal grow | Temperature: 293 K / pH: 8.5 Details: 30% methyl-pentanediol, 0.1M Tris pH 8.5, 0.2M sodium chloride, 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 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 22, 2013 / Details: K-B FOCUSING MIRRORS |
Radiation | Monochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→48.023 Å / Num. obs: 13444 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rsym value: 0.04 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.12→2.24 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.499 / % possible all: 84.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IQ6 Resolution: 2.12→48.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0 / SU B: 18.957 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 65.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→48.02 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 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.12→2.18 Å / Total num. of bins used: 20
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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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