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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pvr
TitleThe Phenylacetyl-CoA monooxygenase PaaAC subcomplex with benzoyl-CoA
Components
  • Phenylacetic acid degradation protein paaA
  • Phenylacetic acid degradation protein paaC
KeywordsOXIDOREDUCTASE / protein-protein complex / ferretin-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
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)95,52411
Polymers94,0083
Non-polymers1,5168
Water7,476415
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)132,64518
Polymers129,7964
Non-polymers2,84814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area13900 Å2
ΔGint-72 kcal/mol
Surface area41580 Å2
MethodPISA
2
B: Phenylacetic acid degradation protein paaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2022
Polymers29,1101
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.631, 77.631, 300.688
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-276-

HOH

-
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-BYC / benzoyl coenzyme A


Mass: 871.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H40N7O17P3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
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

-
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: 2.1→37.586 Å / Num. obs: 54874 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.078 / Χ2: 0.905 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.06-2.134.20.43355060.806196.6
2.13-2.225.10.35157150.706199.4
2.22-2.325.30.30656740.853199.6
2.32-2.445.70.22657420.7081100
2.44-2.65.90.16557600.681100
2.6-2.860.12657810.7171100
2.8-3.086.20.08958070.6761100
3.08-3.526.50.06358530.8191100
3.52-4.446.70.06159161.713199.8
4.44-506.70.03862831.111199.5

-
Phasing

PhasingMethod: molecular replacement

-
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: 2.1→37.586 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2053 / WRfactor Rwork: 0.1713 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8558 / SU B: 10.397 / SU ML: 0.123 / SU R Cruickshank DPI: 0.2093 / SU Rfree: 0.1734 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 2782 5.1 %RANDOM
Rwork0.1878 ---
obs0.1897 54874 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.63 Å2 / Biso mean: 36.6476 Å2 / Biso min: 14.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 98 415 6781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226494
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9558787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8885785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36424.018336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.513151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2521556
X-RAY DIFFRACTIONr_chiral_restr0.0810.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215009
X-RAY DIFFRACTIONr_mcbond_it0.5341.53906
X-RAY DIFFRACTIONr_mcangle_it0.98326215
X-RAY DIFFRACTIONr_scbond_it1.63732588
X-RAY DIFFRACTIONr_scangle_it2.674.52572
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 188 -
Rwork0.247 3750 -
all-3938 -
obs--98.8 %
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)
10.64690.2058-0.39260.5813-0.33071.0472-0.00470.13030.03-0.1265-0.0015-0.0751-0.07390.04140.00610.1222-0.0040.00050.06230.00350.0492-34.94645.342-29.873
21.89180.1420.14520.77990.07211.1094-0.02420.0083-0.1021-0.05340.0028-0.17240.13010.28190.02130.06590.03880.01920.10440.01250.0427-21.12328.095-1.706
32.2688-0.8749-0.46494.20440.29052.3869-0.08940.0515-0.32660.1016-0.03920.39550.1755-0.13130.12860.1351-0.01040.01250.1474-0.0830.2021-35.03313.169-41.216
410.4324-2.6618-0.01352.86963.81196.6301-0.1823-0.1048-0.53360.25720.10880.18330.36980.15510.07350.15830.01150.04450.05150.03410.1008-35.55851.414-32.616
51.07970.1169-0.59320.0151-0.06460.32910.1087-0.09640.1776-0.0135-0.01670.0372-0.02990.0406-0.0920.4972-0.0587-0.11510.2670.01140.2723-31.51536.791-19.031
60.1694-0.1222-0.03070.1626-0.00080.6897-0.00850.0615-0.0409-0.0590.0014-0.03840.01610.10180.0070.1618-0.02210.00890.15750.00190.1682-31.62335.188-21.043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 302
2X-RAY DIFFRACTION2C1 - 248
3X-RAY DIFFRACTION3B1 - 236
4X-RAY DIFFRACTION4A310
5X-RAY DIFFRACTION5A311 - 313
6X-RAY DIFFRACTION5B249
7X-RAY DIFFRACTION5C249 - 251
8X-RAY DIFFRACTION6A314 - 517
9X-RAY DIFFRACTION6B351 - 415
10X-RAY DIFFRACTION6C252 - 398

+
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