[English] 日本語
Yorodumi
- PDB-1l7d: Crystal Structure of R. rubrum Transhydrogenase Domain I without ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l7d
TitleCrystal Structure of R. rubrum Transhydrogenase Domain I without Bound NAD(H)
Componentsnicotinamide nucleotide Transhydrogenase, subunit alpha 1
KeywordsOXIDOREDUCTASE / Transhydrogenase domain I
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 / protein dimerization activity
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
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: 1.81 Å
AuthorsPrasad, G.S. / Wahlberg, M. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal Structures of Transhydrogenase Domain I with and without Bound NADH
Authors: Prasad, G.S. / Wahlberg, M. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D.
History
DepositionMar 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
B: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
C: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
D: nicotinamide nucleotide Transhydrogenase, subunit alpha 1


Theoretical massNumber of molelcules
Total (without water)161,2994
Polymers161,2994
Non-polymers00
Water16,916939
1
A: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
B: nicotinamide nucleotide Transhydrogenase, subunit alpha 1


Theoretical massNumber of molelcules
Total (without water)80,6502
Polymers80,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-21 kcal/mol
Surface area28900 Å2
MethodPISA
2
C: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
D: nicotinamide nucleotide Transhydrogenase, subunit alpha 1


Theoretical massNumber of molelcules
Total (without water)80,6502
Polymers80,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-19 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.96, 117.13, 94.23
Angle α, β, γ (deg.)90., 108.26, 90.
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
nicotinamide nucleotide Transhydrogenase, subunit alpha 1 / / Transhydrogenase Domain I


Mass: 40324.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q60164, UniProt: Q2RSB2*PLUS, EC: 1.6.1.1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: mPEG 2K, Tris-HCl, Magnesium acetate, pH 7.5, VAPOR DIFFUSION, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
310 mMammonium sulfate1drop
41 mMdithiothreitol1drop
50.5 mMPMSF1drop
618 %(w/v)PEG20001reservoir
7100 mMTris-HCl1reservoirpH7.5
81 mMmagnesium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 29, 2000
RadiationMonochromator: Curved crystal (silicon 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. all: 209505 / Num. obs: 113060 / % possible obs: 91.2 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.076 / Net I/σ(I): 8.5
Reflection shellResolution: 1.81→1.86 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.433 / % possible all: 66.6
Reflection
*PLUS
Num. measured all: 209505 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.5

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.81→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 3389 Random
Rwork0.22 --
all0.22 113060 -
obs0.22 112959 -
Refinement stepCycle: LAST / Resolution: 1.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10405 0 0 939 11344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.27
Refinement
*PLUS
Highest resolution: 1.82 Å / Rfactor Rwork: 0.22
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://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