[English] 日本語
Yorodumi
- PDB-6owe: Enoyl-CoA carboxylases/reductases in complex with ethylmalonyl CoA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6owe
TitleEnoyl-CoA carboxylases/reductases in complex with ethylmalonyl CoA
ComponentsCrotonyl-CoA carboxylase/reductase
KeywordsOXIDOREDUCTASE / ECR / highly efficient CO2-fixing enzyme
Function / homology
Function and homology information


crotonyl-CoA reductase activity / NADPH:quinone reductase activity / NADPH binding / mRNA 3'-UTR binding / cytosol
Similarity search - Function
Crotonyl-CoA reductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...Crotonyl-CoA reductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Chem-N9V / Chem-NDP / Putative crotonyl-CoA reductase
Similarity search - Component
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsDeMirci, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Four amino acids define the CO2binding pocket of enoyl-CoA carboxylases/reductases.
Authors: Stoffel, G.M.M. / Saez, D.A. / DeMirci, H. / Vogeli, B. / Rao, Y. / Zarzycki, J. / Yoshikuni, Y. / Wakatsuki, S. / Vohringer-Martinez, E. / Erb, T.J.
History
DepositionMay 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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: Crotonyl-CoA carboxylase/reductase
B: Crotonyl-CoA carboxylase/reductase
C: Crotonyl-CoA carboxylase/reductase
D: Crotonyl-CoA carboxylase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,90714
Polymers196,8904
Non-polymers5,01710
Water20,0331112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22430 Å2
ΔGint-41 kcal/mol
Surface area59800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.100, 78.700, 138.900
Angle α, β, γ (deg.)90.00, 108.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Crotonyl-CoA carboxylase/reductase


Mass: 49222.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054) (bacteria)
Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054
Gene: ccr1, KSE_56510 / Production host: Escherichia coli (E. coli) / References: UniProt: E4N096
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-N9V / 5'-O-[(S)-{[(S)-[(3R)-4-({(1E)-3-[(2-{[(2S)-2-carboxybutanoyl]sulfanyl}ethyl)amino]-3-oxoprop-1-en-1-yl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine 3'-(dihydrogen phosphate)


Mass: 879.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H40N7O19P3S
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1112 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 8
Details: 100 mM TRIS pH 8.0 and 20% w/v poly (acrylic acid sodium salt) 5100

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. obs: 230524 / % possible obs: 97.24 % / Redundancy: 3.34 % / Net I/σ(I): 4.7
Reflection shellResolution: 1.72→1.78 Å / Num. unique obs: 24347

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→29.894 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 17.93
RfactorNum. reflection% reflection
Rfree0.1704 1201 0.52 %
Rwork0.1572 --
obs0.1573 230524 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→29.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13789 0 324 1112 15225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414710
X-RAY DIFFRACTIONf_angle_d1.23420030
X-RAY DIFFRACTIONf_dihedral_angle_d24.5885325
X-RAY DIFFRACTIONf_chiral_restr0.0832137
X-RAY DIFFRACTIONf_plane_restr0.0082604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.78890.26631290.250524347X-RAY DIFFRACTION93
1.7889-1.87030.23051260.20824694X-RAY DIFFRACTION95
1.8703-1.96890.20721290.181124926X-RAY DIFFRACTION95
1.9689-2.09220.17191340.15325544X-RAY DIFFRACTION98
2.0922-2.25370.20051340.153425818X-RAY DIFFRACTION99
2.2537-2.48040.17361370.159625948X-RAY DIFFRACTION99
2.4804-2.8390.17581390.162825801X-RAY DIFFRACTION98
2.839-3.57590.16991350.159726103X-RAY DIFFRACTION99
3.5759-29.89880.1361380.133626142X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -16.7647 Å / Origin y: -1.4129 Å / Origin z: -33.0094 Å
111213212223313233
T0.183 Å20.0117 Å2-0.0137 Å2-0.1803 Å20.0054 Å2--0.1781 Å2
L0.1358 °20.0033 °2-0.0863 °2-0.194 °20.022 °2--0.2204 °2
S-0.004 Å °0.0016 Å °-0.0036 Å °-0.0136 Å °0.0059 Å °-0.0019 Å °0.0156 Å °0.0235 Å °-0.0016 Å °
Refinement TLS groupSelection details: all

+
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