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- PDB-6era: Crystal structure of cyclohexanone monooxygenase mutant (F249A, F... -

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Basic information

Entry
Database: PDB / ID: 6era
TitleCrystal structure of cyclohexanone monooxygenase mutant (F249A, F280A and F435A) from Rhodococcus sp. Phi1 bound to NADP+
ComponentsCyclohexanone monooxygenase
KeywordsFLAVOPROTEIN / Monooxygenase / Rossmann fold / FAD / NADP+ / lactone / dihydrocarvone
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Cyclohexanone monooxygenase
Similarity search - Component
Biological speciesRhodococcus sp. Phi1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsKaruppiah, V. / Scrutton, N.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/M013219/1 United Kingdom
CitationJournal: Biochemistry / Year: 2018
Title: Biocatalytic Routes to Lactone Monomers for Polymer Production.
Authors: Messiha, H.L. / Ahmed, S.T. / Karuppiah, V. / Suardiaz, R. / Ascue Avalos, G.A. / Fey, N. / Yeates, S. / Toogood, H.S. / Mulholland, A.J. / Scrutton, N.S.
History
DepositionOct 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclohexanone monooxygenase
B: Cyclohexanone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4816
Polymers121,4232
Non-polymers3,0584
Water2,468137
1
A: Cyclohexanone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2403
Polymers60,7111
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclohexanone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2403
Polymers60,7111
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.860, 64.940, 187.590
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyclohexanone monooxygenase


Mass: 60711.430 Da / Num. of mol.: 2 / Mutation: F249A, F280A, F435A
Source method: isolated from a genetically manipulated source
Details: Mutations - F249A, F280A and F435A / Source: (gene. exp.) Rhodococcus sp. Phi1 (bacteria) / Gene: chnB / Production host: Escherichia coli (E. coli) / References: UniProt: Q84H73
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.49→62.06 Å / Num. obs: 45368 / % possible obs: 99.8 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.045 / Net I/σ(I): 9.9
Reflection shellResolution: 2.49→2.53 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2228 / CC1/2: 0.587 / Rpim(I) all: 0.525 / % possible all: 99.9

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GWD

3gwd


Resolution: 2.49→62.06 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.74 / Phase error: 29.77
RfactorNum. reflection% reflection
Rfree0.2617 2167 4.78 %
Rwork0.214 --
obs0.2163 45335 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.49→62.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8186 0 202 137 8525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058612
X-RAY DIFFRACTIONf_angle_d0.71911778
X-RAY DIFFRACTIONf_dihedral_angle_d3.2035047
X-RAY DIFFRACTIONf_chiral_restr0.0471283
X-RAY DIFFRACTIONf_plane_restr0.0051637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4901-2.5480.38511410.31252860X-RAY DIFFRACTION100
2.548-2.61170.35811160.30362869X-RAY DIFFRACTION100
2.6117-2.68230.3431730.28472857X-RAY DIFFRACTION100
2.6823-2.76120.32421370.27082824X-RAY DIFFRACTION100
2.7612-2.85040.29211650.26422875X-RAY DIFFRACTION100
2.8504-2.95220.31781500.26622824X-RAY DIFFRACTION100
2.9522-3.07040.33961440.26942869X-RAY DIFFRACTION100
3.0704-3.21020.33341290.2622884X-RAY DIFFRACTION100
3.2102-3.37940.31431380.2362890X-RAY DIFFRACTION100
3.3794-3.59110.28551490.22032885X-RAY DIFFRACTION100
3.5911-3.86840.24581690.20752844X-RAY DIFFRACTION100
3.8684-4.25760.21541370.18662873X-RAY DIFFRACTION100
4.2576-4.87340.22351310.16732912X-RAY DIFFRACTION100
4.8734-6.13920.21131420.20032911X-RAY DIFFRACTION100
6.1392-62.07920.2571460.19892991X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.42580.0122-0.90361.0258-0.13881.66840.1215-0.16490.07220.1485-0.0835-0.142-0.12220.2484-0.04440.3082-0.0244-0.01470.3965-0.01170.440457.887914.162972.0295
21.3368-0.09120.03362.27950.73491.68790.06150.2902-0.1101-0.81230.062-0.13670.2689-0.3149-0.10990.8723-0.07880.01220.5781-0.04820.532137.5121-14.078123.6015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 536)
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 535)

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