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- PDB-6er9: Crystal structure of cyclohexanone monooxygenase from Rhodococcus... -

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Basic information

Entry
Database: PDB / ID: 6er9
TitleCrystal structure of cyclohexanone monooxygenase 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: 2.37 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

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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)124,9376
Polymers121,8792
Non-polymers3,0584
Water2,774154
1
A: Cyclohexanone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4693
Polymers60,9401
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclohexanone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4693
Polymers60,9401
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.080, 64.440, 186.220
Angle α, β, γ (deg.)90.00, 96.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyclohexanone monooxygenase


Mass: 60939.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 154 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.37→92.6 Å / Num. obs: 51521 / % possible obs: 98.8 % / Redundancy: 3.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.07 / Net I/σ(I): 7.9
Reflection shellResolution: 2.37→2.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3797 / CC1/2: 0.523 / Rpim(I) all: 0.614 / % possible all: 99.6

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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: 2.37→92.597 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.97
RfactorNum. reflection% reflection
Rfree0.2456 2605 5.06 %
Rwork0.1998 --
obs0.2021 51485 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.37→92.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8320 0 202 154 8676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068756
X-RAY DIFFRACTIONf_angle_d0.81211973
X-RAY DIFFRACTIONf_dihedral_angle_d3.4615124
X-RAY DIFFRACTIONf_chiral_restr0.0511295
X-RAY DIFFRACTIONf_plane_restr0.0051666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.41310.3951490.31592555X-RAY DIFFRACTION99
2.4131-2.45950.34441490.30592615X-RAY DIFFRACTION100
2.4595-2.50970.31671260.28672489X-RAY DIFFRACTION99
2.5097-2.56430.34991580.27262613X-RAY DIFFRACTION100
2.5643-2.6240.32481210.26092571X-RAY DIFFRACTION99
2.624-2.68960.34111370.26122606X-RAY DIFFRACTION99
2.6896-2.76230.30061030.2612538X-RAY DIFFRACTION99
2.7623-2.84360.31331350.25922598X-RAY DIFFRACTION99
2.8436-2.93540.36221530.25262536X-RAY DIFFRACTION99
2.9354-3.04030.27231300.25012596X-RAY DIFFRACTION99
3.0403-3.1620.27071450.23392585X-RAY DIFFRACTION100
3.162-3.3060.26581210.22032584X-RAY DIFFRACTION100
3.306-3.48030.26471210.20582581X-RAY DIFFRACTION99
3.4803-3.69830.24951410.19392600X-RAY DIFFRACTION99
3.6983-3.98390.21381370.1762560X-RAY DIFFRACTION98
3.9839-4.38480.20191480.16142509X-RAY DIFFRACTION97
4.3848-5.01920.19271570.15262528X-RAY DIFFRACTION97
5.0192-6.32350.20491300.18012575X-RAY DIFFRACTION97
6.3235-92.66720.2181440.16692641X-RAY DIFFRACTION97
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)
11.5742-0.2019-1.12671.07860.01162.06960.195-0.14060.17680.0095-0.036-0.2321-0.29140.3201-0.12210.2862-0.0480.00790.3668-0.03850.4385.60729.971871.7165
21.3341-0.29080.1712.31010.84661.51530.16370.2712-0.2328-1.0143-0.02410.07070.1049-0.1428-0.13940.8934-0.0203-0.08930.5142-0.06350.457637.5516-17.041422.9945
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 536)

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