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- PDB-3pw8: The Phenylacetyl-CoA monooxygenase PaaAC subcomplex with acetyl-CoA -

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Basic information

Entry
Database: PDB / ID: 3pw8
TitleThe Phenylacetyl-CoA monooxygenase PaaAC subcomplex with acetyl-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
ACETYL 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: 2.97 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 paaC
B: Phenylacetic acid degradation protein paaC
C: Phenylacetic acid degradation protein paaA
D: Phenylacetic acid degradation protein paaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,4156
Polymers129,7964
Non-polymers1,6192
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13980 Å2
ΔGint-78 kcal/mol
Surface area41270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.796, 122.796, 153.756
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTRPTRP2AA2 - 24813 - 259
21ASNASNTRPTRP2BB2 - 24813 - 259
12THRTHRLYSLYS2CC2 - 3024 - 304
22THRTHRLYSLYS2DD2 - 3024 - 304
13ACOACOACOACO1CE310
23ACOACOACOACO1DF310

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 35788.535 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: 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
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S

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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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium citrate, 15% PEG6000, pH 5.5, 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: May 24, 2010
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: 2.97→46.17 Å / Num. obs: 27887 / % possible obs: 99 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.97-3.026.30.68199.6
3.02-3.086.30.54699.6
3.08-3.146.30.51199.9
3.14-3.26.30.44299.7
3.2-3.276.30.36699.4
3.27-3.346.30.30199.3
3.34-3.436.40.26699.5
3.43-3.526.30.22499.5
3.52-3.626.30.19199.5
3.62-3.746.30.18999.2
3.74-3.886.30.1699.1
3.88-4.036.30.1499.3
4.03-4.216.30.11599
4.21-4.446.30.09898.9
4.44-4.716.30.08498.9
4.71-5.086.30.08898.8
5.08-5.596.30.11998.4
5.59-6.396.20.1198
6.39-8.056.20.06497.6
8.05-505.90.03496.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PVT
Resolution: 2.97→46.17 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25916 1403 5 %RANDOM
Rwork0.20646 ---
obs0.20906 26487 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.295 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å2-1.19 Å20 Å2
2---2.38 Å20 Å2
3---3.57 Å2
Refinement stepCycle: LAST / Resolution: 2.97→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8686 0 102 0 8788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228984
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9512191
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96251092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80324.074459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.806151475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0231573
X-RAY DIFFRACTIONr_chiral_restr0.0840.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216965
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4631.55444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90128659
X-RAY DIFFRACTIONr_scbond_it1.26933540
X-RAY DIFFRACTIONr_scangle_it2.2634.53532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A988TIGHT POSITIONAL0.140.05
1A933MEDIUM POSITIONAL0.260.5
1A988TIGHT THERMAL0.270.5
1A933MEDIUM THERMAL0.432
2C1204TIGHT POSITIONAL0.030.05
2C1165MEDIUM POSITIONAL0.150.5
2C1204TIGHT THERMAL0.050.5
2C1165MEDIUM THERMAL0.062
3C51TIGHT POSITIONAL0.290.05
3C51TIGHT THERMAL0.090.5
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 104 -
Rwork0.298 1910 -
obs--97.96 %

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