[English] 日本語
Yorodumi
- PDB-8uaj: Succinate Bound Crystal Structure of Thermus scotoductus SA-01 En... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uaj
TitleSuccinate Bound Crystal Structure of Thermus scotoductus SA-01 Ene-reductase
ComponentsNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / SUCCINIC ACID / NADPH dehydrogenase
Similarity search - Component
Biological speciesThermus scotoductus SA-01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsWilson, L.A. / Guddat, L. / Schenk, G. / Scott, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
CitationJournal: Catalysts / Year: 2024
Title: Structural Characterization of Enzymatic Interactions with Functional Nicotinamide Cofactor Biomimetics
Authors: Rocha, R.A. / Wilson, L.A. / Schwartz, B.D. / Warden, A.C. / Guddat, L.W. / Speight, R.E. / Malins, L. / Schenk, G. / Scott, C.
History
DepositionSep 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADPH dehydrogenase
B: NADPH dehydrogenase
C: NADPH dehydrogenase
D: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,08712
Polymers160,7894
Non-polymers2,2988
Water14,646813
1
A: NADPH dehydrogenase
hetero molecules

A: NADPH dehydrogenase
hetero molecules

C: NADPH dehydrogenase
hetero molecules

C: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,08712
Polymers160,7894
Non-polymers2,2988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
Buried area13640 Å2
ΔGint-46 kcal/mol
Surface area44940 Å2
MethodPISA
2
B: NADPH dehydrogenase
hetero molecules

B: NADPH dehydrogenase
hetero molecules

D: NADPH dehydrogenase
hetero molecules

D: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,08712
Polymers160,7894
Non-polymers2,2988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_656-x+1,y,-z+11
Buried area13790 Å2
ΔGint-43 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.642, 101.182, 101.182
Angle α, β, γ (deg.)90.00, 113.92, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-550-

HOH

21C-592-

HOH

31C-708-

HOH

-
Components

#1: Protein
NADPH dehydrogenase


Mass: 40197.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus scotoductus SA-01 (bacteria) / Strain: ATCC 700910 / SA-01 / Gene: TSC_p800090 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E8PRF1
#2: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Succinic acid, 0.1 M bicine, 30% MPEG 550

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.13→49.12 Å / Num. obs: 99650 / % possible obs: 97.9 % / Redundancy: 6.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.066 / Rrim(I) all: 0.166 / Χ2: 0.46 / Net I/σ(I): 8.6 / Num. measured all: 649720
Reflection shellResolution: 2.13→2.17 Å / % possible obs: 60.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.675 / Num. measured all: 16197 / Num. unique obs: 3013 / CC1/2: 0.732 / Rpim(I) all: 0.3 / Rrim(I) all: 0.742 / Χ2: 0.27 / Net I/σ(I) obs: 1.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→49.12 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 1994 2.01 %
Rwork0.1749 --
obs0.1753 99393 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10728 0 156 813 11697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211296
X-RAY DIFFRACTIONf_angle_d0.6215410
X-RAY DIFFRACTIONf_dihedral_angle_d7.4981630
X-RAY DIFFRACTIONf_chiral_restr0.0421686
X-RAY DIFFRACTIONf_plane_restr0.0052022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.190.27131250.24666332X-RAY DIFFRACTION90
2.19-2.250.24311410.19546992X-RAY DIFFRACTION100
2.25-2.320.20371480.18636954X-RAY DIFFRACTION100
2.32-2.390.20261410.17946982X-RAY DIFFRACTION100
2.39-2.480.20481460.17867010X-RAY DIFFRACTION100
2.48-2.580.21591410.17946946X-RAY DIFFRACTION100
2.58-2.70.23781430.18246986X-RAY DIFFRACTION100
2.7-2.840.21161410.18056990X-RAY DIFFRACTION100
2.84-3.020.21561460.18127017X-RAY DIFFRACTION100
3.02-3.250.19581380.17856990X-RAY DIFFRACTION100
3.25-3.570.21661440.16967009X-RAY DIFFRACTION100
3.57-4.090.16571440.15857022X-RAY DIFFRACTION100
4.09-5.150.16091460.14967050X-RAY DIFFRACTION100
5.15-49.120.18821500.18447119X-RAY DIFFRACTION99

+
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