[English] 日本語
Yorodumi
- PDB-6cy8: Crystal structure of FAD-dependent dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cy8
TitleCrystal structure of FAD-dependent dehydrogenase
Components
  • Alpha/beta hydrolase fold proteinAlpha/beta hydrolase superfamily
  • Butyryl-CoA dehydrogenaseShort-chain acyl-CoA dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / acyl carrier protein / FAD-dependent enzyme / natural product biosynthesis
Function / homology
Function and homology information


short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / flavin adenine dinucleotide binding / hydrolase activity
Similarity search - Function
Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain ...Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Alpha/beta hydrolase family / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Alpha/beta hydrolase fold-1 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 4'-PHOSPHOPANTETHEINE / Alpha/beta hydrolase fold protein / Butyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesMarinomonas mediterranea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.729 Å
AuthorsAgarwal, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R00ES026620 United States
CitationJournal: Biochemistry / Year: 2019
Title: Insights into Thiotemplated Pyrrole Biosynthesis Gained from the Crystal Structure of Flavin-Dependent Oxidase in Complex with Carrier Protein.
Authors: Thapa, H.R. / Robbins, J.M. / Moore, B.S. / Agarwal, V.
History
DepositionApr 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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
B: Butyryl-CoA dehydrogenase
A: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4414
Polymers50,2972
Non-polymers1,1442
Water1,964109
1
B: Butyryl-CoA dehydrogenase
A: Alpha/beta hydrolase fold protein
hetero molecules

B: Butyryl-CoA dehydrogenase
A: Alpha/beta hydrolase fold protein
hetero molecules

B: Butyryl-CoA dehydrogenase
A: Alpha/beta hydrolase fold protein
hetero molecules

B: Butyryl-CoA dehydrogenase
A: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,76216
Polymers201,1878
Non-polymers4,5768
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area32350 Å2
ΔGint-240 kcal/mol
Surface area59110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.365, 104.365, 235.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Butyryl-CoA dehydrogenase / Short-chain acyl-CoA dehydrogenase


Mass: 41703.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1) (bacteria)
Strain: ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1 / Gene: Marme_4091 / Production host: Escherichia coli (E. coli)
References: UniProt: F2K077, short-chain acyl-CoA dehydrogenase
#2: Protein Alpha/beta hydrolase fold protein / Alpha/beta hydrolase superfamily


Mass: 8592.757 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1) (bacteria)
Strain: ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1 / Gene: Marme_4088 / Production host: Escherichia coli (E. coli) / References: UniProt: F2K074
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.68 Å3/Da / Density % sol: 66.61 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. obs: 19969 / % possible obs: 95.9 % / Redundancy: 11.5 % / Net I/σ(I): 12.52
Reflection shellResolution: 2.7→2.75 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 2.729→42.195 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 985 4.97 %RANDOM
Rwork0.1912 ---
obs0.1937 19799 94.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.729→42.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 75 109 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083570
X-RAY DIFFRACTIONf_angle_d0.9664851
X-RAY DIFFRACTIONf_dihedral_angle_d4.892838
X-RAY DIFFRACTIONf_chiral_restr0.055537
X-RAY DIFFRACTIONf_plane_restr0.005623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7293-2.87310.29741070.20652471X-RAY DIFFRACTION88
2.8731-3.05310.28131250.22012714X-RAY DIFFRACTION97
3.0531-3.28870.25591460.20172706X-RAY DIFFRACTION97
3.2887-3.61950.26851500.19072691X-RAY DIFFRACTION96
3.6195-4.14290.20711340.1772718X-RAY DIFFRACTION96
4.1429-5.21810.19731560.16382717X-RAY DIFFRACTION95
5.2181-42.19980.25551670.20672797X-RAY DIFFRACTION92

+
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