[English] 日本語
Yorodumi
- PDB-6jls: Crystal Structure of FMN-dependent Cysteine Decarboxylases TvaF f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jls
TitleCrystal Structure of FMN-dependent Cysteine Decarboxylases TvaF from Thioviridamide Biosynthesis
ComponentsPutative flavoprotein decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / FMN-dependent
Function / homologyFlavoprotein / Flavin prenyltransferase-like / Flavoprotein / catalytic activity / FLAVIN MONONUCLEOTIDE / Phosphopantothenoylcysteine decarboxylase
Function and homology information
Biological speciesStreptomyces olivoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsLi, J. / Lu, J. / Wang, H. / Zhu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Org.Lett. / Year: 2019
Title: Characterization of the FMN-Dependent Cysteine Decarboxylase from Thioviridamide Biosynthesis.
Authors: Lu, J. / Li, J. / Wu, Y. / Fang, X. / Zhu, J. / Wang, H.
History
DepositionMar 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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: Putative flavoprotein decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8612
Polymers20,4041
Non-polymers4561
Water1,11762
1
A: Putative flavoprotein decarboxylase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)250,32624
Polymers244,85012
Non-polymers5,47612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation27_555-x+1/2,y,-z+1/21
crystal symmetry operation32_555-z+1/2,x,-y+1/21
crystal symmetry operation34_555-y+1/2,z,-x+1/21
crystal symmetry operation50_555-x+1/2,-y+1/2,z1
crystal symmetry operation55_555-z+1/2,-x+1/2,y1
crystal symmetry operation60_555-y+1/2,-z+1/2,x1
crystal symmetry operation76_555x,-y+1/2,-z+1/21
crystal symmetry operation78_555z,-x+1/2,-y+1/21
crystal symmetry operation83_555y,-z+1/2,-x+1/21
Buried area34000 Å2
ΔGint-268 kcal/mol
Surface area64220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.915, 216.915, 216.915
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

-
Components

#1: Protein Putative flavoprotein decarboxylase


Mass: 20404.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces olivoviridis (bacteria) / Gene: tvaF / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: T2HUM4
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 5.23 Å3/Da / Density % sol: 76.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Two micro liters of protein solution containing 7 mg/ml Tvaf in 20 mM Tris, pH 8.0, 50 mM NaCl, was mixed with 2 micro liters of well solution containing 0.1 M Sodium chloride, 0.1M Bicine ...Details: Two micro liters of protein solution containing 7 mg/ml Tvaf in 20 mM Tris, pH 8.0, 50 mM NaCl, was mixed with 2 micro liters of well solution containing 0.1 M Sodium chloride, 0.1M Bicine pH 9.0, and 30% PEG 500 MME (vol/vol). The crystallization drop was incubated against 100 micro liters of well solution.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.24→76.691 Å / Num. obs: 21611 / % possible obs: 100 % / Redundancy: 29.8 % / CC1/2: 0.999 / Net I/σ(I): 11.5
Reflection shellResolution: 2.24→2.31 Å / Num. unique obs: 1937 / CC1/2: 0.395

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3235: ???)refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G63

1g63


Resolution: 2.24→76.691 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 1124 5.21 %
Rwork0.2158 --
obs0.2166 21582 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→76.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 0 62 1252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071212
X-RAY DIFFRACTIONf_angle_d0.891662
X-RAY DIFFRACTIONf_dihedral_angle_d13.521718
X-RAY DIFFRACTIONf_chiral_restr0.056205
X-RAY DIFFRACTIONf_plane_restr0.006208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2402-2.34210.37261310.38562495X-RAY DIFFRACTION100
2.3421-2.46560.33781470.32152476X-RAY DIFFRACTION100
2.4656-2.62010.34331470.29882504X-RAY DIFFRACTION100
2.6201-2.82240.26381300.24662532X-RAY DIFFRACTION100
2.8224-3.10640.23961500.21912513X-RAY DIFFRACTION100
3.1064-3.5560.20171320.18532568X-RAY DIFFRACTION100
3.556-4.48010.16141470.15912582X-RAY DIFFRACTION100
4.4801-76.7360.20941400.18562788X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 83.5922 Å / Origin y: 69.3499 Å / Origin z: 49.3223 Å
111213212223313233
T0.2941 Å2-0.0624 Å20.0262 Å2-0.314 Å20.106 Å2--0.2696 Å2
L0.6986 °20.0586 °20.4458 °2-2.2527 °2-0.9515 °2--1.7952 °2
S-0.0261 Å °-0.1029 Å °0.1233 Å °0.245 Å °-0.0127 Å °-0.1791 Å °-0.1207 Å °0.2289 Å °0.048 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://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