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- PDB-3uox: Crystal Structure of OTEMO (FAD bound form 2) -

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Basic information

Entry
Database: PDB / ID: 3uox
TitleCrystal Structure of OTEMO (FAD bound form 2)
ComponentsOTEMO
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 / 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.956 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)124,4634
Polymers122,8922
Non-polymers1,5712
Water7,296405
1
A: OTEMO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2312
Polymers61,4461
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OTEMO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2312
Polymers61,4461
Non-polymers7861
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)67.318, 92.540, 93.350
Angle α, β, γ (deg.)90.000, 103.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein OTEMO


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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG3350, 0.1 M sodium/potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 18, 2010
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.956→90.857 Å / Num. obs: 79134 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.098 / Χ2: 1.713 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.956-2.022.80.54178091.067198.4
2.02-2.12.80.42378511.225198.4
2.1-2.22.90.30478711.174199
2.2-2.312.90.2679241.352199.3
2.31-2.4630.19479191.284199.7
2.46-2.653.10.15679751.411199.9
2.65-2.913.20.12479791.774199.8
2.91-3.333.30.09779562.541199.4
3.33-4.23.30.06580023.021199.5
4.2-90.8573.30.03878481.797196.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UOV

3uov


Resolution: 1.956→48.156 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2073 / WRfactor Rwork: 0.1731 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8453 / SU B: 3.928 / SU ML: 0.113 / SU R Cruickshank DPI: 0.1834 / SU Rfree: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 3967 5 %RANDOM
Rwork0.1902 ---
obs0.1922 78981 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.56 Å2 / Biso mean: 24.0837 Å2 / Biso min: 9.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å2-0.36 Å2
2--1.59 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.956→48.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8507 0 106 405 9018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228856
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.95812057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16151069
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93123.364431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.262151387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2041572
X-RAY DIFFRACTIONr_chiral_restr0.10.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216890
X-RAY DIFFRACTIONr_mcbond_it0.8631.55321
X-RAY DIFFRACTIONr_mcangle_it1.61328574
X-RAY DIFFRACTIONr_scbond_it2.57633535
X-RAY DIFFRACTIONr_scangle_it4.1544.53481
LS refinement shellResolution: 1.956→2.007 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 249 -
Rwork0.248 5009 -
all-5258 -
obs--88.91 %

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