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Yorodumi- PDB-2oo5: Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oo5 | ||||||
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Title | Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex | ||||||
Components | (NAD(P) transhydrogenase subunit ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / NAD(H)-binding site / NADP(H)-binding site | ||||||
Function / homology | Function and homology information NAD(P)+ transhydrogenase (Si-specific) activity / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADH binding / NAD+ binding / NAD binding / NADP binding / protein dimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Rhodospirillum rubrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Bhakta, T. / Jackson, J.B. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structures of the dI(2)dIII(1) Complex of Proton-Translocating Transhydrogenase with Bound, Inactive Analogues of NADH and NADPH Reveal Active Site Geometries Authors: Bhakta, T. / Whitehead, S.J. / Snaith, J.S. / Dafforn, T.R. / Wilkie, J. / Rajesh, S. / White, S.A. / Jackson, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oo5.cif.gz | 314.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oo5.ent.gz | 258.2 KB | Display | PDB format |
PDBx/mmJSON format | 2oo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oo5_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2oo5_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2oo5_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 2oo5_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/2oo5 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/2oo5 | HTTPS FTP |
-Related structure data
Related structure data | 2oorC 1u2dS 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
-NAD(P) transhydrogenase subunit ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 40324.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: pntAA, nntA1 / Plasmid: pCD1 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 References: UniProt: P0C186, UniProt: Q2RSB2*PLUS, EC: 1.6.1.2 #2: Protein | | Mass: 18749.463 Da / Num. of mol.: 1 / Fragment: residues 262-464 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: pntB, nntB / Plasmid: pNIC2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0C188, EC: 1.6.1.2 |
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-Non-polymers , 4 types, 34 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-NAP / | #6: 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: 2.38 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8 Details: 18% PEG 4000, 10% glycerol, 100mM Tris, 75mM lithium sulphate, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→80.163 Å / Num. obs: 27548 / % possible obs: 92.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 7.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U2D Resolution: 2.6→80.06 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.859 / SU B: 21.556 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.39 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.228 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→80.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 48.9347 Å / Origin y: 55.9314 Å / Origin z: 119.4688 Å
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL
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