[English] 日本語
Yorodumi
- PDB-1f8g: THE X-RAY STRUCTURE OF NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f8g
TitleTHE X-RAY STRUCTURE OF NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE FROM RHODOSPIRILLUM RUBRUM COMPLEXED WITH NAD+
ComponentsNICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
KeywordsOXIDOREDUCTASE / Nucleotide fold / Proton pump Transhydrogenase / Rossmann fold
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
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 ...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 / 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 / NAD(P) transhydrogenase subunit alpha part 1 / NAD(P) transhydrogenase subunit alpha part 1
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsBuckley, P.A. / Baz Jackson, J. / Schneider, T. / White, S.A. / Rice, D.W. / Baker, P.J.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Protein-protein recognition, hydride transfer and proton pumping in the transhydrogenase complex.
Authors: Buckley, P.A. / Baz Jackson, J. / Schneider, T. / White, S.A. / Rice, D.W. / Baker, P.J.
#1: Journal: To be Published
Title: The Crystallization of the dI Component of Transhydrogenase, A Proton-Translocating Membrane Protein
Authors: Sedelnikova, S.E. / Burke, J. / Buckley, P.A. / Rice, D.W. / Jackson, J.B. / Cotton, N.P.J. / Grindley, R.L. / Baker, P.J.
History
DepositionJun 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine
Item: _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
B: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
C: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
D: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7678
Polymers164,1134
Non-polymers2,6544
Water26,2841459
1
A: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
C: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3834
Polymers82,0562
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-31 kcal/mol
Surface area29820 Å2
MethodPISA
2
B: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
D: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3834
Polymers82,0562
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-29 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.900, 116.600, 102.000
Angle α, β, γ (deg.)90.00, 104.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer. Two are present in asymmetric unit, chains A and C and chains B and D.

-
Components

#1: Protein
NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE


Mass: 41028.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Plasmid: PCD1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q60164, UniProt: Q2RSB2*PLUS, EC: 1.6.1.1
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1459 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM NAD (+), 25% methylethyl PEG 2000, 200mM sodium phosphate buffer, pH7.5, 30mM Ammonium sulphate. , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Sedelnikova, S.E., (2000) Acta Crystallogr., D56, 1170.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-22 mg/mlprotein1drop
210 mMsodium phosphate1drop
330 mMammonium sulfate1drop
410 mMNAD+1drop
5200 mMsodium phosphate1reservoir
630 mMammonium sulfate1reservoir
710-20 %mPEG20001reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM30A10.9796
SYNCHROTRONESRF BM30A20.9794
SYNCHROTRONESRF BM30A30.9686
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEOct 30, 1999
MARRESEARCH2IMAGE PLATEOct 30, 1999
MARRESEARCH3IMAGE PLATEOct 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97941
30.96861
ReflectionResolution: 2→20 Å / Num. all: 99140 / Num. obs: 99140 / % possible obs: 94.7 % / Redundancy: 3.22 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.271 / Num. unique all: 5966 / % possible all: 89.4
Reflection
*PLUS
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.5

-
Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.26 4776 5% random
Rwork0.21 --
all-90649 -
obs-90649 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11116 0 158 1459 12733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d0.025
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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