[English] 日本語
Yorodumi
- PDB-6kri: Crystal Structure of Acyl-CoA Dehydrogenase FadE5 from Mycobacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kri
TitleCrystal Structure of Acyl-CoA Dehydrogenase FadE5 from Mycobacteria smegmatis with product released
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


: / long-chain acyl-CoA dehydrogenase / medium-chain acyl-CoA dehydrogenase / long-chain fatty acyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / medium-chain fatty acyl-CoA dehydrogenase activity / short-chain fatty acyl-CoA dehydrogenase activity / fatty acid metabolic process / flavin adenine dinucleotide binding / plasma membrane
Similarity search - Function
Acyl-CoA dehydrogenase, N-terminal, bacteria / : / Acetyl-CoA dehydrogenase-like C-terminal domain / Acetyl-CoA dehydrogenase C-terminal like / : / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase / Broad-specificity linear acyl-CoA dehydrogenase FadE5
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 Å
AuthorsLiu, X. / Chen, X.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria.
Authors: Chen, X. / Chen, J. / Yan, B. / Zhang, W. / Guddat, L.W. / Liu, X. / Rao, Z.
History
DepositionAug 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: 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 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 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: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,9666
Polymers133,2022
Non-polymers1,7634
Water24,8971382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11890 Å2
ΔGint-88 kcal/mol
Surface area39520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.934, 205.903, 73.951
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-1223-

HOH

21B-1461-

HOH

31B-1483-

HOH

-
Components

#1: Protein Acyl-CoA dehydrogenase


Mass: 66601.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: fadE5, ERS451418_00380 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0D6G5A8, UniProt: Q3L887*PLUS, short-chain acyl-CoA dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1382 / 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: 2.8 Å3/Da / Density % sol: 56.05 % / Mosaicity: 0.377 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5 / Details: 2M (NH4)2SO4, 2% (v/V) PEG400, 0.1M Acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 194416 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.054 / Rrim(I) all: 0.14 / Χ2: 0.966 / Net I/σ(I): 5 / Num. measured all: 1263335
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.635.81.28996480.450.5871.4190.9100
1.63-1.666.21.15196660.560.51.2570.918100
1.66-1.696.41.02496210.6340.4341.1140.919100
1.69-1.726.50.90897040.6960.3810.9860.93299.9
1.72-1.766.40.77695890.7490.3290.8450.93999.6
1.76-1.86.10.63895510.7850.2790.6980.96998.3
1.8-1.856.50.53795340.8560.2260.5840.99498.6
1.85-1.96.80.45696880.9020.1880.4941.016100
1.9-1.956.80.3896710.9310.1570.4120.9999.9
1.95-2.026.70.30996740.9520.1280.3350.998100
2.02-2.096.50.25197450.9620.1060.2731.01599.9
2.09-2.176.10.20695760.9670.090.2261.04598.3
2.17-2.276.70.17996670.9770.0740.1941.14799.4
2.27-2.396.80.15297590.9840.0630.1651.019100
2.39-2.546.80.13497640.9850.0550.1461.013100
2.54-2.746.60.11897750.9860.050.1280.99699.9
2.74-3.016.50.10597280.9880.0440.1140.97199.2
3.01-3.456.90.09298750.9910.0380.10.96599.9
3.45-4.346.40.08199110.990.0350.0880.93299.5
4.34-506.60.065102700.9940.0270.070.64599.4

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.604→44.748 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.55
RfactorNum. reflection% reflection
Rfree0.1908 9218 4.94 %
Rwork0.1666 --
obs0.1678 186737 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 279.73 Å2 / Biso mean: 21.5687 Å2 / Biso min: 6.51 Å2
Refinement stepCycle: final / Resolution: 1.604→44.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9277 0 177 1387 10841
Biso mean--33.4 31.42 -
Num. residues----1210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089603
X-RAY DIFFRACTIONf_angle_d0.88313022
X-RAY DIFFRACTIONf_dihedral_angle_d7.4317750
X-RAY DIFFRACTIONf_chiral_restr0.051439
X-RAY DIFFRACTIONf_plane_restr0.0061682
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.604-1.62220.27971480.2724275545
1.6222-1.64130.27181920.2644398164
1.6413-1.66130.29082400.2602514783
1.6613-1.68240.27742860.2424569093
1.6824-1.70450.27193050.2329591097
1.7045-1.72790.24913230.224599398
1.7279-1.75250.26273130.2193605998
1.7525-1.77870.2493190.2147606698
1.7787-1.80650.23592950.2088592096
1.8065-1.83610.22083090.1978594497
1.8361-1.86780.20253180.18436147100
1.8678-1.90170.20433020.18256183100
1.9017-1.93830.20523290.17326120100
1.9383-1.97790.20363250.16986144100
1.9779-2.02090.19453400.1656153100
2.0209-2.06790.18383150.15846162100
2.0679-2.11960.18733180.15596195100
2.1196-2.17690.18383050.1489605598
2.1769-2.2410.17122980.1483616899
2.241-2.31330.173370.14266145100
2.3133-2.3960.18213100.14226202100
2.396-2.49190.18083040.14376196100
2.4919-2.60530.17733410.14166201100
2.6053-2.74260.18223190.14676216100
2.7426-2.91440.17063130.1532616999
2.9144-3.13940.17643550.16066200100
3.1394-3.45520.18363210.15736271100
3.4552-3.9550.1723410.14926315100
3.955-4.98180.15463430.1433629699
4.9818-44.7480.21033540.2054651699

+
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