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- PDB-8am6: Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrifica... -

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Basic information

Entry
Database: PDB / ID: 8am6
TitleCyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 complexed with dehydrogenated substrate cyclohex-2-en-1-one - inactive mutant (Y195F)
ComponentsFumarate reductase/succinate dehydrogenase flavoprotein domain protein
KeywordsFLAVOPROTEIN / FAD / cyclic ketone / enzyme engineering / rational design
Function / homology
Function and homology information


steroid metabolic process / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
cyclohex-2-en-1-one / FLAVIN-ADENINE DINUCLEOTIDE / Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
Similarity search - Component
Biological speciesAlicycliphilus denitrificans K601 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsPrior, S.H. / Taylor, E.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)1065600 United Kingdom
CitationJournal: Chem Sci / Year: 2024
Title: Rational design of a cyclohexanone dehydrogenase for enhanced alpha , beta-desaturation and substrate specificity.
Authors: Singh, W. / Brown, N.L. / McCue, H.V. / Marriott, S.R. / Wilson, R.C. / Perry, J. / Turkenburg, J.P. / Dubey, K.D. / Prior, S.H. / Carnell, A.J. / Taylor, E.J. / Black, G.W.
History
DepositionAug 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
BaB: Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,79848
Polymers129,1072
Non-polymers5,69146
Water23,2751292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Bioinformatics
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15170 Å2
ΔGint-155 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.030, 121.700, 158.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

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Protein , 1 types, 2 molecules AAABaB

#1: Protein Fumarate reductase/succinate dehydrogenase flavoprotein domain protein


Mass: 64553.590 Da / Num. of mol.: 2 / Mutation: Y195F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicycliphilus denitrificans K601 (bacteria)
Gene: Alide2_4318 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4G7N3

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Non-polymers , 5 types, 1338 molecules

#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-A2Q / cyclohex-2-en-1-one / cyclohex-2-enone


Mass: 96.127 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1292 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 240 mM ammonium citrate tribasic 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.33→60.932 Å / Num. obs: 290848 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 1 / Rrim(I) all: 0.15 / Net I/σ(I): 8.3
Reflection shellResolution: 1.33→1.35 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 14363 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
SHELXDEphasing
Cootmodel building
CRANKphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8am3

8am3


Resolution: 1.33→60.932 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.965 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.052
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 14422 4.961 %RANDOM
Rwork0.174 276302 --
all0.175 ---
obs0.175 290724 99.863 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.368 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.33→60.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8264 0 369 1292 9925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0129496
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.63312939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68351234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.4221.538468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.352151495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5731567
X-RAY DIFFRACTIONr_chiral_restr0.1170.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.027490
X-RAY DIFFRACTIONr_nbd_refined0.2230.24846
X-RAY DIFFRACTIONr_nbtor_refined0.3180.26215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.21088
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.247
X-RAY DIFFRACTIONr_mcbond_it1.2611.4154705
X-RAY DIFFRACTIONr_mcangle_it1.7812.1256004
X-RAY DIFFRACTIONr_scbond_it2.6171.6874791
X-RAY DIFFRACTIONr_scangle_it3.6492.4256931
X-RAY DIFFRACTIONr_lrange_it5.25121.27515443
X-RAY DIFFRACTIONr_ncsr_local_group_10.0510.0519144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.3650.35210600.34220184X-RAY DIFFRACTION99.7371
1.365-1.4020.31110590.30919761X-RAY DIFFRACTION99.8801
1.402-1.4430.2910470.2819161X-RAY DIFFRACTION99.8913
1.443-1.4870.2710340.25318624X-RAY DIFFRACTION99.9085
1.487-1.5360.2269530.22118149X-RAY DIFFRACTION99.838
1.536-1.5890.2299000.20317478X-RAY DIFFRACTION99.8479
1.589-1.6490.2018620.18217016X-RAY DIFFRACTION99.8994
1.649-1.7170.1928120.16416286X-RAY DIFFRACTION99.8248
1.717-1.7930.1768240.15515677X-RAY DIFFRACTION99.891
1.793-1.880.1687560.1514975X-RAY DIFFRACTION99.816
1.88-1.9820.177250.14914310X-RAY DIFFRACTION99.8473
1.982-2.1020.1746690.15613543X-RAY DIFFRACTION99.8735
2.102-2.2470.1726590.15412717X-RAY DIFFRACTION99.8805
2.247-2.4270.1675900.1511914X-RAY DIFFRACTION99.8563
2.427-2.6580.1855500.15910975X-RAY DIFFRACTION99.9306
2.658-2.9710.1815710.1589891X-RAY DIFFRACTION99.9522
2.971-3.4290.1774830.1548798X-RAY DIFFRACTION99.8816
3.429-4.1970.1583870.1377537X-RAY DIFFRACTION99.9117
4.197-5.9210.172990.155881X-RAY DIFFRACTION99.8546

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