[English] 日本語
Yorodumi
- PDB-7yls: Structure of a bacteria protein complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yls
TitleStructure of a bacteria protein complex
Components
  • Aromatic-ring-hydroxylating dioxygenase beta subunit
  • Rieske (2Fe-2S) domain protein
KeywordsMETAL BINDING PROTEIN / a bacteria protein complex / FLAVOPROTEIN
Function / homology
Function and homology information


3-phenylpropionate catabolic process / dioxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding
Similarity search - Function
Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / : / FE2/S2 (INORGANIC) CLUSTER / Rieske (2Fe-2S) domain protein / Aromatic-ring-hydroxylating dioxygenase beta subunit
Similarity search - Component
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Structure of a bacteria protein complex
Authors: Zhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aromatic-ring-hydroxylating dioxygenase beta subunit
B: Rieske (2Fe-2S) domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1108
Polymers68,6092
Non-polymers5016
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-47 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.613, 135.613, 135.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

21A-440-

HOH

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Aromatic-ring-hydroxylating dioxygenase beta subunit


Mass: 18952.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: Vapar_1494 / Production host: Escherichia coli (E. coli) / References: UniProt: C5CSP7
#2: Protein Rieske (2Fe-2S) domain protein


Mass: 49656.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: Vapar_1493 / Production host: Escherichia coli (E. coli) / References: UniProt: C5CSP6

-
Non-polymers , 5 types, 478 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion
Details: 2-Methyl-2,4-pentanediol, Sodium cacodylate trihydrate, Magnesium acetate tetrahydrate, 1,3-Propanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→135.61 Å / Num. obs: 77237 / % possible obs: 99.97 % / Redundancy: 26.8 % / Biso Wilson estimate: 25.23 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.93
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 7635 / CC1/2: 0.888

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 1.8→37.61 Å / SU ML: 0.1186 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4141
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1681 3815 4.94 %
Rwork0.1518 73400 -
obs0.1526 77215 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.88 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 23 472 5279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01294929
X-RAY DIFFRACTIONf_angle_d1.23346674
X-RAY DIFFRACTIONf_chiral_restr0.0668696
X-RAY DIFFRACTIONf_plane_restr0.0161882
X-RAY DIFFRACTIONf_dihedral_angle_d6.5066663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.25871300.20132710X-RAY DIFFRACTION100
1.82-1.840.20321390.18722715X-RAY DIFFRACTION100
1.84-1.870.17611450.17972654X-RAY DIFFRACTION100
1.87-1.90.18891510.18152693X-RAY DIFFRACTION100
1.9-1.920.2238940.17892752X-RAY DIFFRACTION100
1.92-1.950.18391360.16462711X-RAY DIFFRACTION100
1.95-1.990.19241200.16332703X-RAY DIFFRACTION100
1.99-2.020.19951420.15652697X-RAY DIFFRACTION100
2.02-2.060.16681650.14292688X-RAY DIFFRACTION100
2.06-2.10.14611240.14582714X-RAY DIFFRACTION100
2.1-2.140.17281490.14932665X-RAY DIFFRACTION100
2.14-2.190.18791600.14872694X-RAY DIFFRACTION100
2.19-2.240.15851440.15222712X-RAY DIFFRACTION100
2.24-2.290.19741320.1492705X-RAY DIFFRACTION100
2.29-2.360.17471300.15072709X-RAY DIFFRACTION100
2.36-2.420.17351250.15792757X-RAY DIFFRACTION100
2.43-2.50.16571390.14942685X-RAY DIFFRACTION100
2.5-2.590.19791440.15252729X-RAY DIFFRACTION100
2.59-2.70.17451300.15222710X-RAY DIFFRACTION100
2.7-2.820.18071500.14842711X-RAY DIFFRACTION100
2.82-2.970.15331730.152708X-RAY DIFFRACTION100
2.97-3.150.14451510.14882727X-RAY DIFFRACTION100
3.15-3.40.15991620.13952687X-RAY DIFFRACTION100
3.4-3.740.17291530.13722730X-RAY DIFFRACTION100
3.74-4.280.13631560.13092757X-RAY DIFFRACTION100
4.28-5.390.16641310.1392788X-RAY DIFFRACTION99.97
5.39-37.610.17471400.19172889X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: 46.086138973 Å / Origin y: 15.9230939606 Å / Origin z: 44.9212675198 Å
111213212223313233
T0.258814801143 Å20.0743285130377 Å20.0697040021739 Å2-0.16422143571 Å20.0605533343903 Å2--0.22688011976 Å2
L0.673583199732 °2-0.29496997878 °20.0637760961938 °2-0.46615527527 °2-0.149982404152 °2--0.665330753527 °2
S-0.0355572563343 Å °-0.0552778191666 Å °-0.134034718807 Å °0.00687117822263 Å °0.011584318272 Å °0.00848774778571 Å °0.168568255121 Å °0.032273159051 Å °0.00844175972927 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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