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- PDB-8am8: Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrifica... -

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Basic information

Entry
Database: PDB / ID: 8am8
TitleCyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 complexed with dehydrogenated substrate - W113A mutant
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 / DI(HYDROXYETHYL)ETHER / Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
Similarity search - Component
Biological speciesAlicycliphilus denitrificans K601 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 3, 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 1.2Oct 16, 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
BBB: Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
AAA: Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,90919
Polymers128,9092
Non-polymers3,00117
Water11,836657
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Bioinformatics
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-55 kcal/mol
Surface area35690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.051, 90.051, 277.358
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11BBB-1038-

HOH

Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains BBB AAA)

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Components

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Protein , 1 types, 2 molecules BBBAAA

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


Mass: 64454.457 Da / Num. of mol.: 2 / Mutation: W113A
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 , 6 types, 674 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-A2Q / cyclohex-2-en-1-one / cyclohex-2-enone


Mass: 96.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
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: I04-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.85→85.65 Å / Num. obs: 98195 / % possible obs: 99.88 % / Redundancy: 2.6 % / Biso Wilson estimate: 20.861 Å2 / CC1/2: 0.973 / Net I/σ(I): 7
Reflection shellResolution: 1.85→1.88 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4779 / CC1/2: 0.999 / % possible all: 99.2

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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: 1.85→85.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.651 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 4802 4.89 %RANDOM
Rwork0.1731 93390 --
all0.175 ---
obs-98192 99.878 %-
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: 25.769 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å20 Å20 Å2
2---0.002 Å20 Å2
3---0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.85→85.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8173 0 197 657 9027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128615
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.63311681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90251083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2421.507438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.363151348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5991562
X-RAY DIFFRACTIONr_chiral_restr0.0990.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026700
X-RAY DIFFRACTIONr_nbd_refined0.2110.24132
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2690
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3230.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.29
X-RAY DIFFRACTIONr_mcbond_it1.6822.3894305
X-RAY DIFFRACTIONr_mcangle_it2.2943.575385
X-RAY DIFFRACTIONr_scbond_it2.7912.6344310
X-RAY DIFFRACTIONr_scangle_it4.0033.836292
X-RAY DIFFRACTIONr_lrange_it4.85833.14613562
X-RAY DIFFRACTIONr_ncsr_local_group_10.0620.0517672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.333350.2936765X-RAY DIFFRACTION99.398
1.898-1.950.2913500.2746597X-RAY DIFFRACTION99.8276
1.95-2.0060.2763460.2526449X-RAY DIFFRACTION99.7358
2.006-2.0680.2823560.2286217X-RAY DIFFRACTION99.8481
2.068-2.1360.2543080.2156106X-RAY DIFFRACTION99.891
2.136-2.2110.2462810.2025923X-RAY DIFFRACTION99.9356
2.211-2.2940.2462650.1885715X-RAY DIFFRACTION99.8664
2.294-2.3880.2522670.1815488X-RAY DIFFRACTION99.9826
2.388-2.4940.2132890.1665286X-RAY DIFFRACTION99.8925
2.494-2.6150.2212710.1745042X-RAY DIFFRACTION99.9812
2.615-2.7570.2312620.1654800X-RAY DIFFRACTION99.9013
2.757-2.9240.2142140.1644608X-RAY DIFFRACTION99.9793
2.924-3.1250.2232140.1614306X-RAY DIFFRACTION99.9558
3.125-3.3760.2241710.1534069X-RAY DIFFRACTION100
3.376-3.6970.1742030.1473717X-RAY DIFFRACTION100
3.697-4.1330.1631780.1423415X-RAY DIFFRACTION100
4.133-4.770.1711670.1333008X-RAY DIFFRACTION100
4.77-5.8380.1971460.1492579X-RAY DIFFRACTION99.9633
5.838-8.2360.171210.1662050X-RAY DIFFRACTION99.954

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