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- PDB-3pvt: The Phenylacetyl-CoA monooxygenase PaaAC subcomplex with 3-hydrox... -

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Basic information

Entry
Database: PDB / ID: 3pvt
TitleThe Phenylacetyl-CoA monooxygenase PaaAC subcomplex with 3-hydroxybutanoyl-CoA
Components
  • Phenylacetic acid degradation protein paaA
  • Phenylacetic acid degradation protein paaC
KeywordsOXIDOREDUCTASE / protein-protein complex / ferritin-like fold / bacterial multicomponent monooxygenase / structural genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


phenylacetyl-CoA 1,2-epoxidase / phenylacetyl-CoA 1,2-epoxidase complex / phenylacetyl-CoA 1,2-epoxidase activity / phenylacetate catabolic process / cytosol
Similarity search - Function
1,2-phenylacetyl-CoA epoxidase, subunit A / 1,2-phenylacetyl-CoA epoxidase, subunit C / 1,2-phenylacetyl-CoA epoxidase, subunit A/C / Phenylacetic acid catabolic protein / : / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
3-HYDROXYBUTANOYL-COENZYME A / 1,2-phenylacetyl-CoA epoxidase, subunit A / 1,2-phenylacetyl-CoA epoxidase, subunit C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsCygler, M. / Grishin, A.M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Functional Studies of the Escherichia coli Phenylacetyl-CoA Monooxygenase Complex.
Authors: Grishin, A.M. / Ajamian, E. / Tao, L. / Zhang, L. / Menard, R. / Cygler, M.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Phenylacetic acid degradation protein paaA
B: Phenylacetic acid degradation protein paaC
C: Phenylacetic acid degradation protein paaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3229
Polymers94,0083
Non-polymers1,3146
Water6,269348
1
A: Phenylacetic acid degradation protein paaA
C: Phenylacetic acid degradation protein paaC
hetero molecules

A: Phenylacetic acid degradation protein paaA
C: Phenylacetic acid degradation protein paaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,24014
Polymers129,7964
Non-polymers2,44410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area16180 Å2
ΔGint-73 kcal/mol
Surface area41770 Å2
MethodPISA
2
B: Phenylacetic acid degradation protein paaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2022
Polymers29,1101
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.366, 77.366, 301.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-264-

HOH

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Components

#1: Protein Phenylacetic acid degradation protein paaA / Phenylacetyl-CoA ring 1 / 2-epoxidase PaaA


Mass: 35788.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. MG1655 / Gene: b1388, JW1383, paaA, ydbO / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P76077, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Protein Phenylacetic acid degradation protein paaC / Phenylacetyl-CoA ring 1 / 2-epoxidase PaaC


Mass: 29109.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. MG1655 / Gene: b1390, JW1385, paaC, ydbP / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P76079, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#3: Chemical ChemComp-3HC / 3-HYDROXYBUTANOYL-COENZYME A / 3-HYDROXYBUTYRYL-COENZYME A


Mass: 853.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N7O18P3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM PIPES, 5% PEG550 MME, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 17, 2009
RadiationMonochromator: DCM with cryo-cooled 1st crystal sagitally bent 2nd crystal followed by vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.03→42.133 Å / Num. obs: 59960 / % possible obs: 99.3 % / Redundancy: 10 % / Rmerge(I) obs: 0.063 / Χ2: 1.179 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.03-2.14.10.38256030.74294.8
2.1-2.195.60.31859010.68699.3
2.19-2.297.40.30659651.00599.9
2.29-2.4110.80.22259380.831100
2.41-2.5611.80.16259760.831100
2.56-2.7611.70.11560390.879100
2.76-3.0311.80.08160100.893100
3.03-3.4711.70.05360721.06399.9
3.47-4.3711.50.05161571.91599.6
4.37-5012.40.04465192.10399.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OTK

1otk


Resolution: 2.03→42.133 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2189 / WRfactor Rwork: 0.1838 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7962 / SU B: 10.419 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1909 / SU Rfree: 0.1634 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 3029 5.1 %RANDOM
Rwork0.1954 ---
obs0.1972 59960 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.3 Å2 / Biso mean: 49.4133 Å2 / Biso min: 26.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--1.27 Å20 Å2
3----2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.03→42.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6269 0 84 348 6701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216482
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9548775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8025786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9724335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.715151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1681556
X-RAY DIFFRACTIONr_chiral_restr0.1090.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215002
X-RAY DIFFRACTIONr_mcbond_it0.6061.53911
X-RAY DIFFRACTIONr_mcangle_it1.14826221
X-RAY DIFFRACTIONr_scbond_it1.93332571
X-RAY DIFFRACTIONr_scangle_it3.1454.52554
LS refinement shellResolution: 2.03→2.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 207 -
Rwork0.321 3898 -
all-4105 -
obs--93.98 %
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)
10.68120.1836-0.36950.5714-0.3020.97920.01380.10750.0236-0.0933-0.0154-0.0645-0.03550.03230.00160.13680.0014-0.0040.05560.00220.0496-34.69945.234-29.898
22.2691-0.8347-0.36124.65150.14722.684-0.0909-0.0115-0.308-0.03990.00480.36880.1842-0.02990.0860.15870.01840.00790.1313-0.05640.1641-34.86713.123-41.347
31.77750.16650.19950.6478-0.08611.1737-0.0106-0.0291-0.0998-0.0908-0.0234-0.13810.17550.24530.03410.09220.03340.02540.11210.01190.0325-20.86128.045-1.7
415.2723-3.49021.77556.06739.373618.3652-0.34550.17-0.8330.54670.05660.39840.82660.18790.28890.123-0.01530.06050.04690.01990.0912-35.52751.893-33.464
50.2334-0.1316-0.04720.1515-0.15870.63640.00490.0304-0.0316-0.0674-0.0274-0.02340.04630.09930.02240.1991-0.00880.01030.1576-0.00380.1578-31.52335.529-19.909
65.51510.30211.1840.3020.50231.01480.2784-0.0964-0.04790.0342-0.2054-0.070.1795-0.2983-0.07290.5813-0.00090.08150.13970.07890.2878-34.928.233-16.675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 302
2X-RAY DIFFRACTION2B1 - 237
3X-RAY DIFFRACTION3C1 - 248
4X-RAY DIFFRACTION4A1 - 310
5X-RAY DIFFRACTION5A - C1 - 349
6X-RAY DIFFRACTION6B - A1 - 311

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