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- PDB-6gqi: Thermocrispum municipale cyclohexanone monooxygenase bound to hex... -

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Basic information

Entry
Database: PDB / ID: 6gqi
TitleThermocrispum municipale cyclohexanone monooxygenase bound to hexanoic acid
ComponentsCyclohexanone Monooxygenase from Thermocrispum municipale
KeywordsFLAVOPROTEIN / Substrate specificity / biocatalysis / protein engineering
Function / homology
Function and homology information


cyclohexanone monooxygenase / cyclohexanone monooxygenase activity / nucleotide binding
Similarity search - Function
: / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 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
HEXANOIC ACID / ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Cyclohexanone Monooxygenase from Thermocrispum municipale
Similarity search - Component
Biological speciesThermocrispum municipale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMattevi, A. / Gomez Castellanos, J.R.
Funding support Italy, 1items
OrganizationGrant numberCountry
European CommissionH2020-LEIT BIO-2014-1 Italy
CitationJournal: ACS Catal / Year: 2018
Title: Side-Chain Pruning Has Limited Impact on Substrate Preference in a Promiscuous Enzyme.
Authors: Furst, M.J.L.J. / Romero, E. / Gomez Castellanos, J.R. / Fraaije, M.W. / Mattevi, A.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 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 from Thermocrispum municipale
B: Cyclohexanone Monooxygenase from Thermocrispum municipale
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,85610
Polymers120,3902
Non-polymers3,4658
Water14,412800
1
A: Cyclohexanone Monooxygenase from Thermocrispum municipale
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8995
Polymers60,1951
Non-polymers1,7044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclohexanone Monooxygenase from Thermocrispum municipale
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9565
Polymers60,1951
Non-polymers1,7614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.069, 93.690, 159.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cyclohexanone Monooxygenase from Thermocrispum municipale


Mass: 60195.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrispum municipale (bacteria) / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A1L1QK40, cyclohexanone monooxygenase

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Non-polymers , 5 types, 808 molecules

#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: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 800 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 100 mM Tris-HCl, 30 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→44.4 Å / Num. obs: 65972 / % possible obs: 99.7 % / Redundancy: 4.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.148 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4617 / CC1/2: 0.65 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M10

5m10


Resolution: 2→44.4 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.299 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19946 3307 5 %RANDOM
Rwork0.13878 ---
obs0.14178 62601 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0 Å2
2---0.46 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8288 0 230 800 9318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0198804
X-RAY DIFFRACTIONr_bond_other_d0.0020.027847
X-RAY DIFFRACTIONr_angle_refined_deg2.1971.97612010
X-RAY DIFFRACTIONr_angle_other_deg1.189318152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7251074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84323.619420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.687151350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8381570
X-RAY DIFFRACTIONr_chiral_restr0.1310.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219912
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021930
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8582.1774276
X-RAY DIFFRACTIONr_mcbond_other3.8392.1754270
X-RAY DIFFRACTIONr_mcangle_it4.5493.2615349
X-RAY DIFFRACTIONr_mcangle_other4.5483.2615348
X-RAY DIFFRACTIONr_scbond_it4.7782.4754528
X-RAY DIFFRACTIONr_scbond_other4.7782.4754529
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5173.5916660
X-RAY DIFFRACTIONr_long_range_B_refined5.73826.72110810
X-RAY DIFFRACTIONr_long_range_B_other5.60226.42710654
X-RAY DIFFRACTIONr_rigid_bond_restr5.374316651
X-RAY DIFFRACTIONr_sphericity_free34.3475411
X-RAY DIFFRACTIONr_sphericity_bonded13.017516819
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 250 -
Rwork0.227 4601 -
obs--99.43 %

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