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- PDB-8hk0: Crystal structure of Fic32-33 complex from Streptomyces ficellus ... -

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Basic information

Entry
Database: PDB / ID: 8hk0
TitleCrystal structure of Fic32-33 complex from Streptomyces ficellus NRRL 8067
Components
  • Acyl-CoA dehydrogenase
  • Dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dehydrogenase / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesStreptomyces ficellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsCheng, Y. / Qiao, H. / Liu, W. / Fang, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778064 China
National Natural Science Foundation of China (NSFC)21977107 China
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Oxidase Heterotetramer Completes 1-Azabicyclo[3.1.0]hexane Formation with the Association of a Nonribosomal Peptide Synthetase.
Authors: Cheng, Y. / Yi, X. / Zhang, Y. / He, Q. / Chen, D. / Cao, W. / Fang, P. / Liu, W.
History
DepositionNov 24, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Dehydrogenase
D: Dehydrogenase
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,4727
Polymers158,6634
Non-polymers1,8093
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17010 Å2
ΔGint-119 kcal/mol
Surface area50120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.080, 137.080, 148.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

#1: Protein Dehydrogenase


Mass: 38132.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ficellus (bacteria) / Gene: EIZ62_06145 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W5T2G8
#2: Protein Acyl-CoA dehydrogenase / Dehydrogenase


Mass: 41199.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ficellus (bacteria) / Gene: EIZ62_06140 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W5T3Z2
#3: 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
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate and 36% w/v PEG2000 MME (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.29→41.6 Å / Num. obs: 63948 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.999 / Net I/σ(I): 16.5
Reflection shellResolution: 2.29→2.35 Å / Num. unique obs: 4640 / CC1/2: 0.833

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→38.44 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 3267 5.11 %
Rwork0.183 --
obs0.186 63915 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10415 0 122 225 10762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410750
X-RAY DIFFRACTIONf_angle_d1.13914690
X-RAY DIFFRACTIONf_dihedral_angle_d17.9393747
X-RAY DIFFRACTIONf_chiral_restr0.1041693
X-RAY DIFFRACTIONf_plane_restr0.0081940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.32420.28791360.23822608X-RAY DIFFRACTION100
2.3242-2.36050.29331370.23422577X-RAY DIFFRACTION100
2.3605-2.39920.30821540.22982598X-RAY DIFFRACTION100
2.3992-2.44060.3051350.23072576X-RAY DIFFRACTION100
2.4406-2.4850.29121410.22882615X-RAY DIFFRACTION100
2.485-2.53280.29091260.23272618X-RAY DIFFRACTION100
2.5328-2.58440.31561310.23182624X-RAY DIFFRACTION100
2.5844-2.64060.27581360.2252609X-RAY DIFFRACTION100
2.6406-2.7020.29721220.22872600X-RAY DIFFRACTION100
2.702-2.76960.30881440.22132635X-RAY DIFFRACTION100
2.7696-2.84450.27961370.22292601X-RAY DIFFRACTION100
2.8445-2.92810.26981500.2292613X-RAY DIFFRACTION100
2.9281-3.02260.31211680.22552595X-RAY DIFFRACTION100
3.0226-3.13060.26451510.22452604X-RAY DIFFRACTION100
3.1306-3.25590.25511340.22072633X-RAY DIFFRACTION100
3.2559-3.4040.2621300.21332649X-RAY DIFFRACTION100
3.404-3.58330.27031240.19652670X-RAY DIFFRACTION100
3.5833-3.80760.23051540.17552636X-RAY DIFFRACTION100
3.8076-4.10130.18771630.16082629X-RAY DIFFRACTION100
4.1013-4.51350.19121350.14412680X-RAY DIFFRACTION100
4.5135-5.16520.16721360.14452703X-RAY DIFFRACTION100
5.1652-6.50250.18931580.17712723X-RAY DIFFRACTION100
6.5025-38.440.17031650.14152852X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -26.4846 Å / Origin y: 25.808 Å / Origin z: -36.7971 Å
111213212223313233
T0.3468 Å20.0242 Å2-0.019 Å2-0.3622 Å2-0.012 Å2--0.3802 Å2
L0.3968 °20.0726 °2-0.0197 °2-0.3399 °20.0131 °2--0.4724 °2
S-0.0274 Å °0.0075 Å °-0.0162 Å °0.0217 Å °0.0131 Å °-0.0356 Å °0.0165 Å °0.0828 Å °0.0161 Å °
Refinement TLS groupSelection details: ALL

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