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- PDB-3pvr: The Phenylacetyl-CoA monooxygenase PaaAC subcomplex with benzoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 3pvr
TitleThe Phenylacetyl-CoA monooxygenase PaaAC subcomplex with benzoyl-CoA
Components
  • Phenylacetic acid degradation protein paaA
  • Phenylacetic acid degradation protein paaC
KeywordsOXIDOREDUCTASE / protein-protein complex / ferretin-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
benzoyl 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: 2.1 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 1.2Jan 22, 2014Group: Refinement description
Revision 1.3Sep 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)95,52411
Polymers94,0083
Non-polymers1,5168
Water7,476415
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)132,64518
Polymers129,7964
Non-polymers2,84814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area13900 Å2
ΔGint-72 kcal/mol
Surface area41580 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)77.631, 77.631, 300.688
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-276-

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-BYC / benzoyl coenzyme A / Benzoyl-CoA


Mass: 871.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H40N7O17P3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
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 25, 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: 2.1→37.586 Å / Num. obs: 54874 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.078 / Χ2: 0.905 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.06-2.134.20.43355060.806196.6
2.13-2.225.10.35157150.706199.4
2.22-2.325.30.30656740.853199.6
2.32-2.445.70.22657420.7081100
2.44-2.65.90.16557600.681100
2.6-2.860.12657810.7171100
2.8-3.086.20.08958070.6761100
3.08-3.526.50.06358530.8191100
3.52-4.446.70.06159161.713199.8
4.44-506.70.03862831.111199.5

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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-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OTK

1otk


Resolution: 2.1→37.586 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2053 / WRfactor Rwork: 0.1713 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8558 / SU B: 10.397 / SU ML: 0.123 / SU R Cruickshank DPI: 0.2093 / SU Rfree: 0.1734 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 2782 5.1 %RANDOM
Rwork0.1878 ---
obs0.1897 54874 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.63 Å2 / Biso mean: 36.6476 Å2 / Biso min: 14.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 98 415 6781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226494
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9558787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8885785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36424.018336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.513151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2521556
X-RAY DIFFRACTIONr_chiral_restr0.0810.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215009
X-RAY DIFFRACTIONr_mcbond_it0.5341.53906
X-RAY DIFFRACTIONr_mcangle_it0.98326215
X-RAY DIFFRACTIONr_scbond_it1.63732588
X-RAY DIFFRACTIONr_scangle_it2.674.52572
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 188 -
Rwork0.247 3750 -
all-3938 -
obs--98.8 %
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)
10.64690.2058-0.39260.5813-0.33071.0472-0.00470.13030.03-0.1265-0.0015-0.0751-0.07390.04140.00610.1222-0.0040.00050.06230.00350.0492-34.94645.342-29.873
21.89180.1420.14520.77990.07211.1094-0.02420.0083-0.1021-0.05340.0028-0.17240.13010.28190.02130.06590.03880.01920.10440.01250.0427-21.12328.095-1.706
32.2688-0.8749-0.46494.20440.29052.3869-0.08940.0515-0.32660.1016-0.03920.39550.1755-0.13130.12860.1351-0.01040.01250.1474-0.0830.2021-35.03313.169-41.216
410.4324-2.6618-0.01352.86963.81196.6301-0.1823-0.1048-0.53360.25720.10880.18330.36980.15510.07350.15830.01150.04450.05150.03410.1008-35.55851.414-32.616
51.07970.1169-0.59320.0151-0.06460.32910.1087-0.09640.1776-0.0135-0.01670.0372-0.02990.0406-0.0920.4972-0.0587-0.11510.2670.01140.2723-31.51536.791-19.031
60.1694-0.1222-0.03070.1626-0.00080.6897-0.00850.0615-0.0409-0.0590.0014-0.03840.01610.10180.0070.1618-0.02210.00890.15750.00190.1682-31.62335.188-21.043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 302
2X-RAY DIFFRACTION2C1 - 248
3X-RAY DIFFRACTION3B1 - 236
4X-RAY DIFFRACTION4A310
5X-RAY DIFFRACTION5A311 - 313
6X-RAY DIFFRACTION5B249
7X-RAY DIFFRACTION5C249 - 251
8X-RAY DIFFRACTION6A314 - 517
9X-RAY DIFFRACTION6B351 - 415
10X-RAY DIFFRACTION6C252 - 398

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