[English] 日本語
Yorodumi
- PDB-7nf0: T. atroviride Fdc variant TaFdcV in complex with hydroxylated prFMN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nf0
TitleT. atroviride Fdc variant TaFdcV in complex with hydroxylated prFMN
ComponentsFerulic acid decarboxylase 1
KeywordsLYASE / fdc / prfmn / decarboxylase / isobutene production
Function / homology
Function and homology information


phenacrylate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / cytosol
Similarity search - Function
UbiD-like decarboxylase/ferulic acid decarboxylase 1 / : / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain
Similarity search - Domain/homology
ACETATE ION / hydroxylated prenyl-FMN / : / : / NITRATE ION / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesHypocrea atroviridis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSaaret, A. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)695013 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production.
Authors: Saaret, A. / Villiers, B. / Stricher, F. / Anissimova, M. / Cadillon, M. / Spiess, R. / Hay, S. / Leys, D.
History
DepositionFeb 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferulic acid decarboxylase 1
B: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,51212
Polymers114,0402
Non-polymers1,47210
Water14,628812
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-42 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.593, 74.593, 345.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1182-

HOH

21A-1196-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ferulic acid decarboxylase 1 / Phenacrylate decarboxylase


Mass: 57019.812 Da / Num. of mol.: 2
Mutation: E25N N31G G305A D351R K377H P402V F404Y T405M T429A V445P Q448W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea atroviridis (strain ATCC 20476 / IMI 206040) (fungus)
Strain: ATCC 20476 / IMI 206040 / Gene: FDC1, TRIATDRAFT_53567 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9NLP8, phenacrylate decarboxylase

-
Non-polymers , 6 types, 822 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-BYN / hydroxylated prenyl-FMN


Mass: 542.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31N4O10P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Calcium chloride dihydrate, sodium formate, PIPES, PEG smear high (BCS condition screen from Molecular Dimensions)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→63.5 Å / Num. obs: 245351 / % possible obs: 99.7 % / Redundancy: 8.8 % / CC1/2: 1 / Net I/σ(I): 10.4
Reflection shellResolution: 1.35→1.37 Å / Num. unique obs: 11383 / CC1/2: 0.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EV4

6ev4


Resolution: 1.35→63.5 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.842 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18385 12192 5 %RANDOM
Rwork0.16565 ---
obs0.16656 232299 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.618 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.35→63.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7644 0 88 812 8544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0138070
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177624
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.64511026
X-RAY DIFFRACTIONr_angle_other_deg1.5321.57817626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59851024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64522.408382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.148151311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0931548
X-RAY DIFFRACTIONr_chiral_restr0.1090.21064
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029189
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021753
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2941.4674055
X-RAY DIFFRACTIONr_mcbond_other1.2751.4674053
X-RAY DIFFRACTIONr_mcangle_it1.7652.2045092
X-RAY DIFFRACTIONr_mcangle_other1.7652.2045093
X-RAY DIFFRACTIONr_scbond_it2.3521.6744015
X-RAY DIFFRACTIONr_scbond_other2.3531.6754012
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3622.4245935
X-RAY DIFFRACTIONr_long_range_B_refined4.0818.4239181
X-RAY DIFFRACTIONr_long_range_B_other3.98818.0379013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 875 -
Rwork0.28 16184 -
obs--94.69 %

+
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