[English] 日本語
Yorodumi
- PDB-2oor: Structure of transhydrogenase (dI.NAD+)2(dIII.H2NADPH)1 asymmetri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oor
TitleStructure of transhydrogenase (dI.NAD+)2(dIII.H2NADPH)1 asymmetric complex
Components(NAD(P) transhydrogenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / 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 / oxidoreductase activity / plasma membrane
Similarity search - Function
NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain ...NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-TXP / NAD(P) transhydrogenase subunit alpha part 1 / NAD(P) transhydrogenase subunit beta / NAD(P) transhydrogenase subunit alpha part 1
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsBhakta, T. / Jackson, J.B.
CitationJournal: 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
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD(P) transhydrogenase subunit alpha part 1
B: NAD(P) transhydrogenase subunit alpha part 1
C: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5657
Polymers99,3993
Non-polymers2,1664
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-49 kcal/mol
Surface area35430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.194, 74.451, 204.844
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
NAD(P) transhydrogenase subunit ... , 2 types, 3 molecules ABC

#1: Protein NAD(P) transhydrogenase subunit alpha part 1 / E.C.1.6.1.2 / Pyridine nucleotide transhydrogenase subunit alpha 1 / Nicotinamide nucleotide transhydrogenase ...Pyridine nucleotide transhydrogenase subunit alpha 1 / Nicotinamide nucleotide transhydrogenase subunit alpha 1 / Proton-translocating transhydrogenase component 1 / dI


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 NAD(P) transhydrogenase subunit beta / E.C.1.6.1.2 / Pyridine nucleotide transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase ...Pyridine nucleotide transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta / Proton-translocating transhydrogenase NADP(H)-binding component / dIII


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

-
Non-polymers , 4 types, 95 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TXP / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE


Mass: 747.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM Mes, 16% PEG 4K, 10% glycerol, 50mM ammonium sulphate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.32→102.629 Å / Num. obs: 44362 / % possible obs: 91.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.32-2.453.60.3172.31703847260.31769
2.45-2.594.10.2332.92328157450.23386.8
2.59-2.774.10.1644.22322856330.16490.6
2.77-34.10.115.82250655120.1194.8
3-3.284.10.0738.22139752420.07397.5
3.28-3.674.20.04912.32047448420.04999.3
3.67-4.244.40.04113.61892443400.04199.7
4.24-5.194.60.0412.81696837190.0499.8
5.19-7.344.60.0413.51341029160.0499.8
7.34-68.044.10.03813.5699916870.03899

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U2D

1u2d


Resolution: 2.32→102.6 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.88 / SU B: 15.88 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.428 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2530 5.7 %RANDOM
Rwork0.247 ---
obs0.249 44314 90.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.352 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2---0.25 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.32→102.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 134 91 6981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226997
X-RAY DIFFRACTIONr_bond_other_d0.0020.026669
X-RAY DIFFRACTIONr_angle_refined_deg1.3372.0069504
X-RAY DIFFRACTIONr_angle_other_deg0.982315522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46124.788236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.832151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1541536
X-RAY DIFFRACTIONr_chiral_restr0.0680.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027626
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021220
X-RAY DIFFRACTIONr_nbd_refined0.140.31266
X-RAY DIFFRACTIONr_nbd_other0.1290.36537
X-RAY DIFFRACTIONr_nbtor_refined0.1460.53307
X-RAY DIFFRACTIONr_nbtor_other0.0790.53720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.5324
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0550.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1020.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.55
X-RAY DIFFRACTIONr_mcbond_it1.12725876
X-RAY DIFFRACTIONr_mcbond_other0.15221863
X-RAY DIFFRACTIONr_mcangle_it1.32637322
X-RAY DIFFRACTIONr_scbond_it0.70522716
X-RAY DIFFRACTIONr_scangle_it1.09132182
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 128 -
Rwork0.295 2055 -
obs-2183 62.07 %
Refinement TLS params.Method: refined / Origin x: -15.4552 Å / Origin y: -19.2289 Å / Origin z: 23.594 Å
111213212223313233
T-0.1292 Å20.0701 Å2-0.0218 Å2--0.1017 Å2-0.0344 Å2---0.213 Å2
L2.0127 °20.6683 °2-0.4505 °2-0.6291 °2-0.1561 °2--0.8324 °2
S-0.0179 Å °0.2393 Å °0.0294 Å °0.0549 Å °0.1074 Å °0.0297 Å °-0.0792 Å °0.0028 Å °-0.0895 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL

IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA1 - 2691 - 269
2BB1 - 2801 - 280
3CC30 - 2021 - 173

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more