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- PDB-3pw1: The Phenylacetyl-CoA monooxygenase PaaAC subcomplex with phenylac... -

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Basic information

Entry
Database: PDB / ID: 3pw1
TitleThe Phenylacetyl-CoA monooxygenase PaaAC subcomplex with phenylacetyl-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
Phenylacetyl 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: 2.25 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

Downloads & links

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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)95,44610
Polymers94,0083
Non-polymers1,4387
Water5,621312
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)132,48916
Polymers129,7964
Non-polymers2,69212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area13850 Å2
ΔGint-73 kcal/mol
Surface area41620 Å2
MethodPISA
2
B: Phenylacetic acid degradation protein paaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2022
Polymers29,1101
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.617, 77.617, 300.364
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-297-

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-FAQ / Phenylacetyl coenzyme A


Mass: 885.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H42N7O17P3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 48.88 %
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: 2.25→37.553 Å / Num. obs: 44432 / % possible obs: 99.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.098 / Χ2: 0.836 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.335.90.45941460.635194.4
2.33-2.426.30.37943400.634198.4
2.42-2.536.60.31643550.651199.3
2.53-2.676.70.23844030.642199.3
2.67-2.836.90.1943910.65199.7
2.83-3.056.90.14244540.657199.9
3.05-3.367.10.09544830.691100
3.36-3.857.10.06745080.8781100
3.85-4.8570.06946041.8191100
4.85-506.70.04148590.943199.5

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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: 2.25→37.553 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2067 / WRfactor Rwork: 0.1649 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8539 / SU B: 13.228 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2799 / SU Rfree: 0.2132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 2249 5.1 %RANDOM
Rwork0.1856 ---
obs0.188 44432 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.39 Å2 / Biso mean: 34.2665 Å2 / Biso min: 14.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2--1.2 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6269 0 93 312 6674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216491
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9558785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9935786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83624335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.328151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7321556
X-RAY DIFFRACTIONr_chiral_restr0.0850.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215013
X-RAY DIFFRACTIONr_mcbond_it0.461.53911
X-RAY DIFFRACTIONr_mcangle_it0.90926221
X-RAY DIFFRACTIONr_scbond_it1.69632580
X-RAY DIFFRACTIONr_scangle_it2.6984.52564
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 152 -
Rwork0.222 2862 -
all-3014 -
obs--93.46 %
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)
10.78930.2529-0.41020.6265-0.42131.34-0.00910.11070.0312-0.1252-0.0139-0.0736-0.07970.04810.0230.11730.002300.0373-0.00570.0435-35.030545.3454-29.8908
22.22370.20160.19540.9006-0.00911.2454-0.0369-0.029-0.1211-0.08750.0137-0.17140.18260.30360.02330.05070.04230.02560.10.00470.0375-21.090528.0069-1.7283
32.432-0.875-0.13194.57910.01693.3716-0.07440.0207-0.29810.1476-0.02890.36480.1575-0.10380.10330.09480.00040.01540.1167-0.09880.1764-35.005413.235-41.1063
42.4478-4.4986-2.96938.27245.45983.6042-0.17980.0067-0.13040.33870.01090.25730.21360.00450.16890.1476-0.02040.04550.08270.05250.1028-35.638851.342-32.5231
50.8485-0.2964-0.41620.4612-0.26451.1973-0.0294-0.0892-0.0827-0.01-0.05080.0884-0.1210.06250.08030.16780.08440.030.38810.0280.3887-31.535432.6341-16.5136
60.1956-0.081-0.0990.1723-0.07990.6807-0.0030.0548-0.0338-0.0639-0.009-0.03630.05320.08780.01210.1281-0.01720.00790.0846-0.01080.1321-32.706335.4522-20.836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 302
2X-RAY DIFFRACTION2C1 - 248
3X-RAY DIFFRACTION3B1 - 237
4X-RAY DIFFRACTION4A310
5X-RAY DIFFRACTION5A311 - 312
6X-RAY DIFFRACTION5B249
7X-RAY DIFFRACTION5C249 - 251
8X-RAY DIFFRACTION6A313 - 617
9X-RAY DIFFRACTION6C300 - 308

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