[English] 日本語
Yorodumi
- PDB-4j16: Crystal structure of Thermus thermophilus transhydrogenase hetero... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j16
TitleCrystal structure of Thermus thermophilus transhydrogenase heterotrimeric complex of the Alpha1 subunit dimer with the NADP binding domain (domain III) of the Beta subunit
Components
  • NAD(P) transhydrogenase subunit beta
  • NAD/NADP transhydrogenase alpha subunit 1
KeywordsOXIDOREDUCTASE / Soluble components of nicotinamide nucleotide transhydrogenase / Complex of Alpha1 subunit dimer with Domain III of Beta subunit / Alpha1 binds NAD(H) / Domain III binds NADP(H) / Domain III binds to Alpha1 / NAD bound to Alpha1 / NADP bound to Domain III
Function / homology
Function and homology information


proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / oxidoreductase activity / plasma membrane
Similarity search - Function
NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain ...NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TRIETHYLENE GLYCOL / proton-translocating NAD(P)(+) transhydrogenase / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsYamaguchi, M. / Leung, J. / Schurig Briccio, L.A. / Gennis, R.B. / Stout, C.D.
CitationJournal: To be Published
Title: Crystal structure analysis of Thermus thermophilus transhydrogenase soluble domains
Authors: Yamaguchi, M. / Leung, J. / Schurig Briccio, L.A. / Gennis, R.B. / Stout, C.D.
History
DepositionFeb 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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/NADP transhydrogenase alpha subunit 1
B: NAD/NADP transhydrogenase alpha subunit 1
C: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,16110
Polymers101,7213
Non-polymers2,4407
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint-65 kcal/mol
Surface area35210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.616, 75.038, 198.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 3 molecules ABC

#1: Protein NAD/NADP transhydrogenase alpha subunit 1


Mass: 40851.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1780 / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) AcrAB- / References: UniProt: Q72GR8, EC: 1.6.1.2
#2: Protein NAD(P) transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta


Mass: 20018.150 Da / Num. of mol.: 1 / Fragment: Domain III (UNP residues 266-450)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) AcrAB- / References: UniProt: Q72GS0, EC: 1.6.1.2

-
Non-polymers , 6 types, 128 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions MD1-47 Morpheus kit, condition E2: 0.12 M ethylene glycols, 0.1 M pH 6.5 buffers, 30% ethylene glycol + PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.18076 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2011 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 2.4→39.98 Å / Num. all: 38049 / Num. obs: 36638 / % possible obs: 96.29 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 18.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4538 / Rsym value: 0.557 / % possible all: 79.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4IZH, 1PNO

4izh

1pno


Resolution: 2.41→39.98 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 20.836 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.474 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25328 1924 5 %RANDOM
Rwork0.20062 ---
all0.20331 38049 --
obs0.20331 36638 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.41→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6906 0 159 121 7186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197186
X-RAY DIFFRACTIONr_bond_other_d0.0010.027134
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.97612558
X-RAY DIFFRACTIONr_angle_other_deg0.771317250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3917.51828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91923.593270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.609151221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7651557
X-RAY DIFFRACTIONr_chiral_restr0.0710.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114391
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022289
LS refinement shellResolution: 2.41→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 121 -
Rwork0.3 2059 -
obs-2059 75.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1384-0.60290.16122.03710.1581.0630.26970.18770.4855-0.0157-0.19120.0385-0.0616-0.0912-0.07860.04940.03260.11820.040.0790.410719.14910.001-22.677
22.4849-0.8777-0.44151.45010.41171.34320.3030.5157-0.2381-0.139-0.18930.03870.4642-0.0682-0.11370.26960.086-0.08630.1495-0.03560.230635.184-22.29-36.002
32.1053-0.0524-0.62753.0798-0.58392.3363-0.0647-0.04430.01670.111-0.01190.13250.1244-0.1050.07660.0358-0.01410.07670.0179-0.00930.266210.949-8.061.86
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 372
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2B1 - 373
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C274 - 450
6X-RAY DIFFRACTION3C501

+
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