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- PDB-3up5: Crystal Structure of OTEMO complex with FAD and NADP (form 4) -

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Basic information

Entry
Database: PDB / ID: 3up5
TitleCrystal Structure of OTEMO complex with FAD and NADP (form 4)
ComponentsOTEMO(2,2,3-Trimethyl-5-oxocyclopent-3-enyl)acetyl-CoA 1,5-monooxygenase
KeywordsOXIDOREDUCTASE / Baeyer-Villiger monooxygenase
Function / homology
Function and homology information


(2,2,3-trimethyl-5-oxocyclopent-3-enyl)acetyl-CoA 1,5-monooxygenase / (+)-camphor catabolic process / FAD binding / monooxygenase activity / NADP binding / protein homodimerization activity / identical protein 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
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.453 Å
AuthorsShi, R. / Matte, A. / Cygler, M. / Lau, P.
CitationJournal: Appl.Environ.Microbiol. / Year: 2012
Title: Cloning, Baeyer-Villiger biooxidations, and structures of the camphor pathway 2-oxo-{Delta}(3)-4,5,5-trimethylcyclopentenylacetyl-coenzyme A monooxygenase of Pseudomonas putida ATCC 17453.
Authors: Leisch, H. / Shi, R. / Grosse, S. / Morley, K. / Bergeron, H. / Cygler, M. / Iwaki, H. / Hasegawa, Y. / Lau, P.C.
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OTEMO
B: OTEMO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,9506
Polymers122,8922
Non-polymers3,0584
Water5,368298
1
A: OTEMO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9753
Polymers61,4461
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OTEMO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9753
Polymers61,4461
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.837, 94.394, 93.135
Angle α, β, γ (deg.)90.000, 102.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein OTEMO / (2,2,3-Trimethyl-5-oxocyclopent-3-enyl)acetyl-CoA 1,5-monooxygenase


Mass: 61445.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: ATCC 17453 / Gene: otemo / Plasmid: pSD80 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H3JQW0*PLUS, Oxidoreductases
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Nicotinamide adenine dinucleotide phosphate


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


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.34 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG3350, 0.1 M sodium/potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 20, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.453→90.968 Å / Num. obs: 39964 / % possible obs: 96.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.097 / Χ2: 1.49 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.453-2.542.60.34940251.275198.2
2.54-2.642.60.340321.203198.4
2.64-2.762.60.24340771.238198.4
2.76-2.92.60.19840581.222198.1
2.9-3.092.70.15240191.322197.9
3.09-3.322.70.11340441.379197.5
3.32-3.662.70.08739601.766196.4
3.66-4.192.70.07139701.948195.5
4.19-5.282.70.05539051.783194.2
5.28-90.9682.80.04838741.715191.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UOY

3uoy


Resolution: 2.453→48.353 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2164 / WRfactor Rwork: 0.1692 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8431 / SU B: 9.014 / SU ML: 0.203 / SU R Cruickshank DPI: 1.017 / SU Rfree: 0.2909 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.017 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 2017 5.1 %RANDOM
Rwork0.1848 ---
obs0.1874 39933 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.26 Å2 / Biso mean: 25.9167 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å2-0.28 Å2
2--3.69 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.453→48.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8491 0 202 298 8991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228948
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.97112205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18951071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01623.349430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.401151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9541572
X-RAY DIFFRACTIONr_chiral_restr0.1240.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216938
X-RAY DIFFRACTIONr_mcbond_it0.771.55320
X-RAY DIFFRACTIONr_mcangle_it1.42328570
X-RAY DIFFRACTIONr_scbond_it2.47133628
X-RAY DIFFRACTIONr_scangle_it3.8784.53632
LS refinement shellResolution: 2.453→2.517 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 117 -
Rwork0.253 2727 -
all-2844 -
obs--93.34 %

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