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Yorodumi- PDB-4txv: Crystal structure of the mixed disulfide intermediate between thi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4txv | ||||||||||||
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Title | Crystal structure of the mixed disulfide intermediate between thioredoxin-like TlpAs(C110S) and subunit II of cytochrome c oxidase CoxBPD (C233S) | ||||||||||||
Components |
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Keywords | PROTEIN BINDING / thioredoxin / mixed disulphide / cytochrome c oxidase | ||||||||||||
Function / homology | Function and homology information cytochrome complex assembly / disulfide oxidoreductase activity / cytochrome-c oxidase / cytochrome-c oxidase activity / respirasome / ATP synthesis coupled electron transport / copper ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Bradyrhizobium diazoefficiens (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||||||||
Authors | Quade, N. / Abicht, H.K. / Hennecke, H. / Glockshuber, R. | ||||||||||||
Funding support | Switzerland, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2014 Title: How Periplasmic Thioredoxin TlpA Reduces Bacterial Copper Chaperone ScoI and Cytochrome Oxidase Subunit II (CoxB) Prior to Metallation. Authors: Abicht, H.K. / Scharer, M.A. / Quade, N. / Ledermann, R. / Mohorko, E. / Capitani, G. / Hennecke, H. / Glockshuber, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4txv.cif.gz | 146.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4txv.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 4txv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/4txv ftp://data.pdbj.org/pub/pdb/validation_reports/tx/4txv | HTTPS FTP |
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-Related structure data
Related structure data | 4txoC 1jfuS 1m56S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19528.553 Da / Num. of mol.: 2 / Fragment: UNP residues 40-217 / Mutation: C110S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium diazoefficiens (bacteria) Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: tlpA, bll1380 / Production host: Escherichia coli (E. coli) / References: UniProt: P43221 #2: Protein | Mass: 17416.859 Da / Num. of mol.: 2 / Fragment: UNP residues 123-264 / Mutation: C233S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) (bacteria) Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: coxB / Plasmid: pProExHTa-His6-CoxBPDC233S / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H7C6E5, cytochrome-c oxidase #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: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG2000 MME, 0.8M formic acid/NaOH, 0.1 M Na-cacodylate |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 45680 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.48 % / Biso Wilson estimate: 40.055 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Χ2: 0.986 / Net I/σ(I): 13.57 / Num. measured all: 301989 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entriues 1JFU and 1m56 Resolution: 2→65.42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.1921 / WRfactor Rwork: 0.148 / FOM work R set: 0.8397 / SU B: 4.465 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1614 / SU Rfree: 0.1504 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.15 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.15 Å2 / Biso mean: 39.402 Å2 / Biso min: 20.94 Å2
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Refinement step | Cycle: final / Resolution: 2→65.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.05 Å / Total num. of bins used: 20
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