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Yorodumi- PDB-3eh4: Structure of the reduced form of cytochrome ba3 oxidase from Ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eh4 | ||||||
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Title | Structure of the reduced form of cytochrome ba3 oxidase from Thermus thermophilus | ||||||
Components |
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Keywords | OXIDOREDUCTASE / CYTOCHROME BA3 OXIDASE / HEME / INTEGRAL MEMBRANE PROTEIN / COPPER / ELECTRON TRANSPORT / HYDROGEN ION TRANSPORT / ION TRANSPORT / IRON / METAL-BINDING / RESPIRATORY CHAIN / TRANSMEMBRANE / TRANSPORT / FORMYLATION / Cell membrane / Membrane | ||||||
Function / homology | Function and homology information cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Liu, B. / Chen, Y. / Doukov, T. / Soltis, S.M. / Stout, D. / Fee, J.A. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the ...Title: Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Authors: Liu, B. / Chen, Y. / Doukov, T. / Soltis, S.M. / Stout, C.D. / Fee, J.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus Authors: Liu, B. / Luna, M. / Chen, Y. / Stout, D. / Fee, J.A. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus Authors: Hunsicker-Wang, L.M. / Pacoma, R.L. / Chen, Y. / Fee, J.A. / Stout, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eh4.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eh4.ent.gz | 131.2 KB | Display | PDB format |
PDBx/mmJSON format | 3eh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/3eh4 ftp://data.pdbj.org/pub/pdb/validation_reports/eh/3eh4 | HTTPS FTP |
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-Related structure data
Related structure data | 3eh3C 3eh5C 1xmeS 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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3 |
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4 |
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Unit cell |
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-Components
-Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 68987.453 Da / Num. of mol.: 1 / Fragment: UNP residues 2-562 / Mutation: K258R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaA, TTHA1135 / Plasmid: PMK18 / Production host: THERMUS THERMOPHILUS (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ79, cytochrome-c oxidase |
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#2: Protein | Mass: 18349.990 Da / Num. of mol.: 1 / Fragment: UNP residues 3-168 / Mutation: E4Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaB, ctaC, TTHA1134 / Plasmid: PMK18 / Production host: THERMUS THERMOPHILUS (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ80, cytochrome-c oxidase |
-Protein/peptide / Sugars , 2 types, 2 molecules C
#3: Protein/peptide | Mass: 3638.407 Da / Num. of mol.: 1 / Fragment: UNP residues 2-34 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaD, TTHA1133 / Plasmid: PMK18 / Production host: THERMUS THERMOPHILUS (bacteria) / Strain (production host): HB8 / References: UniProt: P82543, cytochrome-c oxidase |
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#8: Sugar | ChemComp-BNG / |
-Non-polymers , 5 types, 49 molecules
#4: Chemical | ChemComp-CU1 / |
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#5: Chemical | ChemComp-HEM / |
#6: Chemical | ChemComp-HAS / |
#7: Chemical | ChemComp-CUA / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.24 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Peg 2000, Bis-tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-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 CCD / Detector: Q315R / Date: Jul 27, 2007 Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing). |
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: 2.6→20 Å / Num. obs: 34723 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 0.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XME Resolution: 2.9→19.96 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 32.617 / SU ML: 0.329 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 105.967 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.974 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -31.849 Å / Origin y: 23.921 Å / Origin z: -0.135 Å
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Refinement TLS group |
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