[English] 日本語
Yorodumi
- PDB-4iit: The Phenylacetyl-CoA monooxygenase PaaABC subcomplex with phenyla... -

+
Open data


ID or keywords:

Loading...

-
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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.

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

-
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

+
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