[English] 日本語
Yorodumi
- PDB-6net: FAD-dependent monooxygenase TropB from T. stipitatus substrate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6net
TitleFAD-dependent monooxygenase TropB from T. stipitatus substrate complex
ComponentsFAD-dependent monooxygenase tropB
KeywordsFLAVOPROTEIN / oxidative dearomatization
Function / homology
Function and homology information


Oxidoreductases / FAD binding / monooxygenase activity / membrane
Similarity search - Function
FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 2,4-dihydroxy-3,6-dimethylbenzaldehyde / FAD-dependent monooxygenase tropB
Similarity search - Component
Biological speciesTalaromyces stipitatus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRodriguez Benitez, A. / Tweedy, S.E. / Baker Dockrey, S.A. / Lukowski, A.L. / Wymore, T. / Khare, D. / Brooks, C.L. / Palfey, B.A. / Smith, J.L. / Narayan, A.R.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124880 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
CitationJournal: Acs Catalysis / Year: 2019
Title: Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization.
Authors: Rodriguez Benitez, A. / Tweedy, S.E. / Baker Dockrey, S.A. / Lukowski, A.L. / Wymore, T. / Khare, D. / Brooks 3rd, C.L. / Palfey, B.A. / Smith, J.L. / Narayan, A.R.H.
History
DepositionDec 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FAD-dependent monooxygenase tropB
B: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,11610
Polymers99,8842
Non-polymers2,2338
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-37 kcal/mol
Surface area34250 Å2
2
A: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0955
Polymers49,9421
Non-polymers1,1534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0215
Polymers49,9421
Non-polymers1,0794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.405, 183.834, 164.234
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein FAD-dependent monooxygenase tropB / Tropolone synthesis protein B


Mass: 49941.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006) (fungus)
Strain: ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006 / Gene: tropB, tsL1, TSTA_117740 / Production host: Escherichia coli (E. coli) / References: UniProt: B8M9J8

-
Non-polymers , 5 types, 133 molecules

#2: Chemical ChemComp-KJY / 2,4-dihydroxy-3,6-dimethylbenzaldehyde


Mass: 166.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H10O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 1.11 M ammonium tartrate dibasic, 6% hexanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.245→45.96 Å / Num. obs: 47286 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 51.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.19 / Net I/σ(I): 1
Reflection shellResolution: 2.245→2.325 Å / Rmerge(I) obs: 2.457 / CC1/2: 0.41

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NES

6nes


Resolution: 2.25→45.96 Å / SU ML: 0.3754 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2893
RfactorNum. reflection% reflection
Rfree0.2399 3845 3.92 %
Rwork0.1832 --
obs0.1855 47257 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 62.05 Å2
Refinement stepCycle: LAST / Resolution: 2.25→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 150 125 6989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01257165
X-RAY DIFFRACTIONf_angle_d1.19319732
X-RAY DIFFRACTIONf_chiral_restr0.05731013
X-RAY DIFFRACTIONf_plane_restr0.0081279
X-RAY DIFFRACTIONf_dihedral_angle_d15.4874162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.270.37071390.34753389X-RAY DIFFRACTION96.34
2.27-2.30.35191410.33053453X-RAY DIFFRACTION99.94
2.3-2.340.3361430.32193522X-RAY DIFFRACTION99.97
2.34-2.370.35821460.29853502X-RAY DIFFRACTION100
2.37-2.40.32571380.29063472X-RAY DIFFRACTION99.97
2.4-2.440.32061470.28683493X-RAY DIFFRACTION100
2.44-2.480.36151380.28983541X-RAY DIFFRACTION99.95
2.48-2.520.3381460.27663521X-RAY DIFFRACTION100
2.52-2.570.3521400.27833406X-RAY DIFFRACTION99.94
2.57-2.620.30451430.26813539X-RAY DIFFRACTION99.97
2.62-2.670.33811440.25833504X-RAY DIFFRACTION99.75
2.67-2.730.38981450.28643532X-RAY DIFFRACTION99.86
2.73-2.790.34131380.29463480X-RAY DIFFRACTION99.97
2.79-2.860.38021400.28233469X-RAY DIFFRACTION99.83
2.86-2.940.29541430.23193493X-RAY DIFFRACTION99.95
2.94-3.030.28561460.2063513X-RAY DIFFRACTION99.97
3.03-3.130.26661420.20533480X-RAY DIFFRACTION100
3.13-3.240.29711410.20573497X-RAY DIFFRACTION99.97
3.24-3.370.28511450.19613550X-RAY DIFFRACTION100
3.37-3.520.25291430.1733491X-RAY DIFFRACTION99.97
3.52-3.710.22711410.16013471X-RAY DIFFRACTION100
3.71-3.940.20021450.15213517X-RAY DIFFRACTION100
3.94-4.240.18471430.13553488X-RAY DIFFRACTION100
4.24-4.670.16581420.12233521X-RAY DIFFRACTION100
4.67-5.340.19961400.12423476X-RAY DIFFRACTION100
5.34-6.730.18271440.14483513X-RAY DIFFRACTION100
6.73-46.230.15151420.13643499X-RAY DIFFRACTION99.86

+
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