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- PDB-4ii4: The Phenylacetyl-CoA monooxygenase - mutant PaaA E49Q K68Q - PaaC... -

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Basic information

Entry
Database: PDB / ID: 4ii4
TitleThe Phenylacetyl-CoA monooxygenase - mutant PaaA E49Q K68Q - PaaC wild type subcomplex with benzoyl-CoA
Components
  • 1,2-phenylacetyl-CoA epoxidase, subunit A
  • 1,2-phenylacetyl-CoA epoxidase, subunit C
KeywordsOXIDOREDUCTASE / protein-protein complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / ferritin-like fold / bacterial multicomponent monooxygenase PaaABCE
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 / isomorphous replacement with 3PW1 / Resolution: 2.799 Å
AuthorsCygler, M. / Grishin, A.M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: To be published
Title: Spatial Organization of Subunits within the Phenylacetyl-CoA Monooxygenase Complex
Authors: Grishin, A.M. / Ajamian, E. / Tao, L. / Bostina, M. / Zhang, L. / Trempe, J. / Menard, R. / Rouiller, I. / Cygler, M.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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: 1,2-phenylacetyl-CoA epoxidase, subunit A
B: 1,2-phenylacetyl-CoA epoxidase, subunit C
C: 1,2-phenylacetyl-CoA epoxidase, subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8774
Polymers94,0063
Non-polymers8721
Water45025
1
A: 1,2-phenylacetyl-CoA epoxidase, subunit A
C: 1,2-phenylacetyl-CoA epoxidase, subunit C
hetero molecules

A: 1,2-phenylacetyl-CoA epoxidase, subunit A
C: 1,2-phenylacetyl-CoA epoxidase, subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5366
Polymers129,7924
Non-polymers1,7432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area10910 Å2
ΔGint-76 kcal/mol
Surface area42550 Å2
MethodPISA
2
B: 1,2-phenylacetyl-CoA epoxidase, subunit C


Theoretical massNumber of molelcules
Total (without water)29,1101
Polymers29,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.595, 77.595, 304.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 1,2-phenylacetyl-CoA epoxidase, subunit A / 1 / 2-phenylacetyl-CoA epoxidase / catalytic subunit alpha / 1 / 2-phenylacetyl-CoA monooxygenase / subunit A


Mass: 35786.500 Da / Num. of mol.: 1 / Mutation: E49Q, K68Q
Source method: isolated from a genetically manipulated source
Details: paaA gene contains mutations that lead to aminoacid changes E49Q, K68Q
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Gene: b1388, JW1383, paaA, ydbO / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76077, phenylacetyl-CoA 1,2-epoxidase
#2: Protein 1,2-phenylacetyl-CoA epoxidase, subunit C / 1 / 2-phenylacetyl-CoA epoxidase / structural subunit beta / 1 / 2-phenylacetyl-CoA monooxygenase / subunit C


Mass: 29109.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% ethylene glycol, pH 8.0, 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 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 10, 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: 2.8→50 Å / Num. obs: 24054 / % possible obs: 99.8 % / Redundancy: 14 % / Rmerge(I) obs: 0.127 / Χ2: 1.709 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.8-2.8514.111581.2281100
2.85-2.914.311771.281100
2.9-2.9614.511701.2911100
2.96-3.0214.411631.2821100
3.02-3.0814.411921.2581100
3.08-3.1514.511661.2621100
3.15-3.2314.412071.2491100
3.23-3.3214.511511.30511000.833
3.32-3.4214.411821.30811000.632
3.42-3.5314.412071.37711000.473
3.53-3.6514.411791.44111000.378
3.65-3.814.311861.50411000.311
3.8-3.9714.211881.64611000.232
3.97-4.1814.112041.8911000.175
4.18-4.4414.112182.11211000.149
4.44-4.7913.912072.4111000.125
4.79-5.2713.612302.598199.80.118
5.27-6.0313.412452.78111000.124
6.03-7.5913.312662.608199.80.074
7.59-5010.813582.528196.90.043

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
DENZOdata reduction
PHENIX1.8_1069refinement
RefinementMethod to determine structure: isomorphous replacement with 3PW1
Starting model: 3PW1

3pw1


Resolution: 2.799→26.638 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.48 / σ(F): 1.33 / Phase error: 32.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 1218 5.11 %
Rwork0.2184 --
obs0.2213 23832 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.41 Å2 / Biso mean: 119.142 Å2 / Biso min: 46.84 Å2
Refinement stepCycle: LAST / Resolution: 2.799→26.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6195 0 46 25 6266
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)
12.53480.7715-0.7342.9138-0.82964.6259-0.25910.91820.4844-0.5992-0.1043-0.3993-1.13780.50140.29640.938-0.2051-0.04171.02060.23360.6922-34.304645.3068-29.8526
23.346-2.4294-0.70517.04341.77062.8807-0.18230.4505-0.92160.3673-0.38611.72690.3953-0.77490.56990.6569-0.09740.19641.4833-0.16691.1164-34.16513.2703-41.4499
34.4471-0.25660.00482.32160.13354.7938-0.164-0.1084-0.10720.2503-0.1819-0.88160.2841.82760.34560.59530.0299-0.05081.15040.24150.7571-20.656328.5541-1.4769
40.24090.29730.15330.85760.64040.5128-0.22560.78760.1762-1.1730.0939-0.2579-0.47790.17580.13141.3531-0.30270.35072.01070.55971.2736-34.945753.2719-34.2332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:302 )A-1 - 302
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:239 )B1 - 239
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:248 )C1 - 248
4X-RAY DIFFRACTION4( CHAIN A AND RESID 401:401 )A401

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