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- PDB-8gqr: Crystal structure of VioD with FAD -

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Basic information

Entry
Database: PDB / ID: 8gqr
TitleCrystal structure of VioD with FAD
ComponentsVioD
KeywordsFLAVOPROTEIN / complex
Function / homology: / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / VioD
Function and homology information
Biological speciesDuganella sp. ZLP-XI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRan, T. / Wang, W. / Xu, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770074 China
CitationJournal: Proteins / Year: 2023
Title: Structural basis for substrate binding and catalytic mechanism of the key enzyme VioD in the violacein synthesis pathway.
Authors: Xu, M. / Xu, D. / Gao, M. / Zhuang, X. / Wang, W. / Sun, B. / Ran, T.
History
DepositionAug 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VioD
B: VioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,32711
Polymers89,0872
Non-polymers2,2409
Water8,791488
1
A: VioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7096
Polymers44,5431
Non-polymers1,1665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6175
Polymers44,5431
Non-polymers1,0744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.603, 100.869, 162.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein VioD


Mass: 44543.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Duganella sp. ZLP-XI (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024AX32
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→19.77 Å / Num. obs: 49417 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.982 / Rpim(I) all: 0.13 / Net I/σ(I): 6.2
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 3951 / CC1/2: 0.499 / Rpim(I) all: 0.677

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C4A

3c4a


Resolution: 2.1→19.77 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2256 --
Rwork0.1903 --
obs-49353 99.53 %
Displacement parametersBiso mean: 26.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5721 0 142 488 6351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796003
X-RAY DIFFRACTIONf_angle_d0.94278176
X-RAY DIFFRACTIONf_chiral_restr0.0548893
X-RAY DIFFRACTIONf_plane_restr0.00571053
X-RAY DIFFRACTIONf_dihedral_angle_d19.62843527

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