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- PDB-6jls: Crystal Structure of FMN-dependent Cysteine Decarboxylases TvaF f... -

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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 / homologyphosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / coenzyme A biosynthetic process / FMN binding / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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.

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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

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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

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