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- PDB-8am3: Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrifica... -

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Basic information

Entry
Database: PDB / ID: 8am3
TitleCyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 - wildtype
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
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
FLAVIN-ADENINE DINUCLEOTIDE / Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
Similarity search - Component
Biological speciesAlicycliphilus denitrificans K601 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 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

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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
BBB: Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0918
Polymers129,1392
Non-polymers1,9516
Water16,394910
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Bioinformatics
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-56 kcal/mol
Surface area36540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.699, 90.699, 278.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

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


Mass: 64569.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicycliphilus denitrificans K601 (bacteria)
Gene: Alide2_4318 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: F4G7N3
#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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.22 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: 1.6 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 1.86→90.7 Å / Num. obs: 97297 / % possible obs: 98.8 % / Redundancy: 5.08 % / CC1/2: 1 / Rrim(I) all: 0.131 / Net I/σ(I): 15.1
Reflection shellResolution: 1.86→1.89 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4025 / CC1/2: 0.4 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHASERphasing
SHELXDEphasing
Cootmodel building
CRANKphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 1.86→86.233 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.222 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 4719 4.885 %RANDOM
Rwork0.1705 91887 --
all0.172 ---
obs-96606 98.16 %-
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: 25.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å2-0 Å2-0 Å2
2--0.001 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.86→86.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8196 0 127 910 9233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128758
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.63311924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62751123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64421.441451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.806151385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4511565
X-RAY DIFFRACTIONr_chiral_restr0.1010.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026908
X-RAY DIFFRACTIONr_nbd_refined0.2080.24114
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25991
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2848
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.221
X-RAY DIFFRACTIONr_mcbond_it1.7292.2714411
X-RAY DIFFRACTIONr_mcangle_it2.3823.3945552
X-RAY DIFFRACTIONr_scbond_it2.7682.5394346
X-RAY DIFFRACTIONr_scangle_it4.0533.6826368
X-RAY DIFFRACTIONr_lrange_it5.17731.75713918
X-RAY DIFFRACTIONr_ncsr_local_group_10.0650.0517939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.9080.3952770.3425681X-RAY DIFFRACTION83.6328
1.908-1.960.353410.3156358X-RAY DIFFRACTION96.0155
1.96-2.0170.3053430.2526429X-RAY DIFFRACTION99.1798
2.017-2.0790.2663530.2166207X-RAY DIFFRACTION99.5297
2.079-2.1470.2333150.1886060X-RAY DIFFRACTION99.5161
2.147-2.2230.2372800.1885901X-RAY DIFFRACTION99.1657
2.223-2.3070.2992560.2265675X-RAY DIFFRACTION98.7677
2.307-2.4010.2092710.1675481X-RAY DIFFRACTION99.6362
2.401-2.5070.1982830.1555258X-RAY DIFFRACTION99.6583
2.507-2.630.2042690.1655041X-RAY DIFFRACTION99.6435
2.63-2.7720.2042630.1614800X-RAY DIFFRACTION99.7439
2.772-2.940.2222150.174602X-RAY DIFFRACTION99.7928
2.94-3.1420.1882130.1574307X-RAY DIFFRACTION99.7352
3.142-3.3940.2051710.1574079X-RAY DIFFRACTION99.9295
3.394-3.7170.1721990.1483694X-RAY DIFFRACTION99.6162
3.717-4.1550.1531760.1313414X-RAY DIFFRACTION99.8331
4.155-4.7960.1571700.123020X-RAY DIFFRACTION99.9373
4.796-5.8690.1531450.1252578X-RAY DIFFRACTION99.9633
5.869-8.2810.1851210.1572051X-RAY DIFFRACTION100

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