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- PDB-4iit: The Phenylacetyl-CoA monooxygenase PaaABC subcomplex with phenyla... -

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Basic information

Entry
Database: PDB / ID: 4iit
TitleThe Phenylacetyl-CoA monooxygenase PaaABC subcomplex with phenylacetyl-CoA
Components
  • Phenylacetate-CoA oxygenase subunit PaaA
  • Phenylacetate-CoA oxygenase subunit PaaB
  • Phenylacetate-CoA oxygenase subunit PaaC
KeywordsOXIDOREDUCTASE / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / ferritin-like fold / bacterial multicomponent monooxygenase
Function / homology
Function and homology information


phenylacetyl-CoA 1,2-epoxidase activity / phenylacetate catabolic process / cytosol
Similarity search - Function
Phenylacetic acid degradation B / Phenylacetyl-CoA epoxidase, subunit B / Phenylacetic acid degradation B / 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-like / Ferritin-like superfamily
Similarity search - Domain/homology
Phenylacetyl coenzyme A / Phenylacetic acid degradation protein / Phenylacetic acid degradation protein / Phenylacetic acid degradation protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.3 Å
AuthorsCygler, M. / Grishin, A.M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Family of phenylacetyl-CoA monooxygenases differs in subunit organization from other monooxygenases.
Authors: Grishin, A.M. / Ajamian, E. / Tao, L. / Bostina, M. / Zhang, L. / Trempe, J.F. / Menard, R. / Rouiller, I. / Cygler, M.
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 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

Downloads & links

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Assembly

Deposited unit
A: Phenylacetate-CoA oxygenase subunit PaaA
B: Phenylacetate-CoA oxygenase subunit PaaB
C: Phenylacetate-CoA oxygenase subunit PaaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3484
Polymers75,4633
Non-polymers8861
Water00
1
A: Phenylacetate-CoA oxygenase subunit PaaA
B: Phenylacetate-CoA oxygenase subunit PaaB
C: Phenylacetate-CoA oxygenase subunit PaaC
hetero molecules

A: Phenylacetate-CoA oxygenase subunit PaaA
B: Phenylacetate-CoA oxygenase subunit PaaB
C: Phenylacetate-CoA oxygenase subunit PaaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,6978
Polymers150,9266
Non-polymers1,7712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area15370 Å2
ΔGint-88 kcal/mol
Surface area47450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.941, 208.941, 86.081
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Detailsbiological heterohexamer unit can be obtained by taking chains A,B and C and apply operation X-Y,-Y,-Z.

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Components

#1: Protein Phenylacetate-CoA oxygenase subunit PaaA


Mass: 36510.094 Da / Num. of mol.: 1 / Fragment: UNP residues 33-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: KPHS_23690, paaA / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A6T8I0, 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 Phenylacetate-CoA oxygenase subunit PaaB


Mass: 10980.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: EAE_20515, paaB / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A6T8I1, 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: Protein Phenylacetate-CoA oxygenase subunit PaaC


Mass: 27972.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: KPN78578_14420, KPN_01471, paaC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A6T8I2, 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
#4: Chemical ChemComp-FAQ / Phenylacetyl coenzyme A


Mass: 885.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H42N7O17P3S

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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: 3.59 Å3/Da / Density % sol: 65.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES pH 6.5, 12% 1-propanol, 10% PEG 5000MME, vapor diffusion, sitting 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: Jan 21, 2011
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: 4.3→50 Å / Num. obs: 7908 / % possible obs: 100 % / Redundancy: 17.8 % / Biso Wilson estimate: 223.33 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
4.3-4.379.7199.7
4.37-4.4511.11100
4.45-4.5412.71100
4.54-4.6314.81100
4.63-4.7316.51100
4.73-4.8417.811000.916
4.84-4.9618.811000.951
4.96-5.119.411000.881
5.1-5.2519.811000.974
5.25-5.4219.511000.789
5.42-5.6119.711000.711
5.61-5.8319.511000.591
5.83-6.119.611000.481
6.1-6.4219.811000.326
6.42-6.8219.611000.249
6.82-7.3519.611000.178
7.35-8.0819.711000.11
8.08-9.2520.311000.069
9.25-11.6319.811000.05
11.63-5017.911000.048

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.29 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.51 Å49.4 Å
Translation4.51 Å49.4 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PW1, chains A and C, 3EGR, chain A

3pw1

3egr


Resolution: 4.3→49.397 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.91 / σ(F): 1.34 / Phase error: 48.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3627 364 4.61 %
Rwork0.2884 --
obs0.2913 7895 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 321.5123 Å2
Refinement stepCycle: LAST / Resolution: 4.3→49.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 33 0 4885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124994
X-RAY DIFFRACTIONf_angle_d1.2436772
X-RAY DIFFRACTIONf_dihedral_angle_d16.6491846
X-RAY DIFFRACTIONf_chiral_restr0.086710
X-RAY DIFFRACTIONf_plane_restr0.006891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2992-4.92080.46751340.39162388X-RAY DIFFRACTION98
4.9208-6.19780.42581180.40552494X-RAY DIFFRACTION100
6.1978-49.40010.31841120.23922649X-RAY DIFFRACTION100
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)
11.40030.5412-0.1196.2959-2.82331.386-0.0708-0.54670.68420.7602-0.6263-0.3447-1.20790.41030.83481.7439-0.176-0.50961.777-0.32761.678583.7105-14.7044-25.5044
25.1729-1.7842-1.78789.665-2.64853.64881.662-1.13830.6671.2691-0.41291.85371.9741-0.4876-0.36973.32650.4467-1.4791.3875-3.2075-0.030774.1569-8.0385-2.6621
39.0004-0.686-6.32133.3249-0.51924.45841.1963-2.39052.16491.0439-0.6049-0.24390.05250.8675-0.19261.90410.0873-0.41922.4019-0.72211.276472.6801-38.49-1.3344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C

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