[English] 日本語
Yorodumi
- PDB-3pwq: The Phenylacetyl-CoA monooxygenase PaaAC subcomplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pwq
TitleThe Phenylacetyl-CoA monooxygenase PaaAC subcomplex
Components
  • Phenylacetic acid degradation protein paaA
  • Phenylacetic acid degradation protein paaC
KeywordsOXIDOREDUCTASE / protein-protein complex / 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 / 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
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: 2.65 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 8, 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 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenylacetic acid degradation protein paaC
C: Phenylacetic acid degradation protein paaA
B: Phenylacetic acid degradation protein paaC
D: Phenylacetic acid degradation protein paaA
E: Phenylacetic acid degradation protein paaC
F: Phenylacetic acid degradation protein paaA
G: Phenylacetic acid degradation protein paaC
H: Phenylacetic acid degradation protein paaA
I: Phenylacetic acid degradation protein paaC
J: Phenylacetic acid degradation protein paaC
K: Phenylacetic acid degradation protein paaC
R: Phenylacetic acid degradation protein paaC


Theoretical massNumber of molelcules
Total (without water)376,03112
Polymers376,03112
Non-polymers00
Water3,909217
1
A: Phenylacetic acid degradation protein paaC
C: Phenylacetic acid degradation protein paaA
B: Phenylacetic acid degradation protein paaC
D: Phenylacetic acid degradation protein paaA


Theoretical massNumber of molelcules
Total (without water)129,7964
Polymers129,7964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Phenylacetic acid degradation protein paaC
F: Phenylacetic acid degradation protein paaA
G: Phenylacetic acid degradation protein paaC
H: Phenylacetic acid degradation protein paaA


Theoretical massNumber of molelcules
Total (without water)129,7964
Polymers129,7964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-75 kcal/mol
Surface area42360 Å2
MethodPISA
3
I: Phenylacetic acid degradation protein paaC


Theoretical massNumber of molelcules
Total (without water)29,1101
Polymers29,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
J: Phenylacetic acid degradation protein paaC


Theoretical massNumber of molelcules
Total (without water)29,1101
Polymers29,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
K: Phenylacetic acid degradation protein paaC


Theoretical massNumber of molelcules
Total (without water)29,1101
Polymers29,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
R: Phenylacetic acid degradation protein paaC


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)110.257, 109.062, 305.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31E
41G
12I
22J
32K
42R
13C
23D
33F
43H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 248
2111B1 - 248
3111E1 - 248
4111G1 - 248
1121I1 - 238
2121J1 - 238
3121K1 - 238
4121R1 - 238
1131C31 - 245
2131D31 - 245
3131F31 - 245
4131H31 - 245
1231C264 - 302
2231D264 - 302
3231F264 - 302
4231H264 - 302

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Phenylacetic acid degradation protein paaC / Phenylacetyl-CoA ring 1 / 2-epoxidase PaaC


Mass: 29109.629 Da / Num. of mol.: 8
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.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Na-ADA, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
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: Dec 16, 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: 2.65→49.2 Å / Num. obs: 107560 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.081 / Χ2: 1.253 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.64-2.7340.547107490.70999.9
2.73-2.845.40.454107340.71299.9
2.84-2.976.70.353108030.736100
2.97-3.136.80.241107740.779100
3.13-3.336.80.163107930.85299.9
3.33-3.586.80.102108041.00899.9
3.58-3.946.90.075108821.22799.9
3.94-4.517.10.056109121.487100
4.51-5.697.40.062110082.15100
5.69-5070.042113962.24499.8

-
Phasing

PhasingMethod: molecular replacement

-
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: 2.65→49.2 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.2496 / WRfactor Rwork: 0.2172 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8059 / SU R Cruickshank DPI: 1.8219 / SU Rfree: 0.3554 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 5363 5 %RANDOM
Rwork0.2341 ---
obs0.2357 107560 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.65 Å2 / Biso mean: 54.7614 Å2 / Biso min: 19.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24587 0 0 217 24804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02125107
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9434031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.52353113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28623.9251274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.122154117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.43415209
X-RAY DIFFRACTIONr_chiral_restr0.0770.23669
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119489
X-RAY DIFFRACTIONr_mcbond_it1.2771.515501
X-RAY DIFFRACTIONr_mcangle_it1.801224576
X-RAY DIFFRACTIONr_scbond_it1.69539606
X-RAY DIFFRACTIONr_scangle_it3.0524.59455
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1919TIGHT POSITIONAL0.140.05
12B1919TIGHT POSITIONAL0.060.05
13E1919TIGHT POSITIONAL0.060.05
14G1919TIGHT POSITIONAL0.090.05
11A1919TIGHT THERMAL0.370.5
12B1919TIGHT THERMAL0.370.5
13E1919TIGHT THERMAL0.370.5
14G1919TIGHT THERMAL1.090.5
21I1763TIGHT POSITIONAL0.10.05
22J1763TIGHT POSITIONAL0.090.05
23K1763TIGHT POSITIONAL0.10.05
24R1763TIGHT POSITIONAL0.140.05
21I1763TIGHT THERMAL0.40.5
22J1763TIGHT THERMAL1.210.5
23K1763TIGHT THERMAL0.410.5
24R1763TIGHT THERMAL0.40.5
31C1951TIGHT POSITIONAL0.080.05
32D1951TIGHT POSITIONAL0.10.05
33F1951TIGHT POSITIONAL0.060.05
34H1951TIGHT POSITIONAL0.050.05
31C1951TIGHT THERMAL0.070.5
32D1951TIGHT THERMAL0.070.5
33F1951TIGHT THERMAL0.070.5
34H1951TIGHT THERMAL0.070.5
LS refinement shellResolution: 2.652→2.721 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 394 -
Rwork0.316 7485 -
all-7879 -
obs--99.56 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more