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- PDB-6ydr: Crystal structure of Mengla Virus VP30 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6ydr
TitleCrystal structure of Mengla Virus VP30 C-terminal domain
ComponentsMinor nucleoprotein VP30
KeywordsVIRAL PROTEIN / Transcription Factor
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm / RNA binding / zinc ion binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1160 / Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator VP30
Similarity search - Component
Biological speciesMengla dianlovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsTomas Gilabert, O. / Ferrero, D.S. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2017-83906-P Spain
CitationJournal: To Be Published
Title: Crystal structure of Mengla Virus VP30 C-terminal domain
Authors: Tomas Gilabert, O. / Ferrero, D.S. / Verdaguer, N.
History
DepositionMar 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9363
Polymers16,7481
Non-polymers1882
Water2,738152
1
A: Minor nucleoprotein VP30
hetero molecules

A: Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8726
Polymers33,4962
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area4510 Å2
ΔGint-48 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.062, 73.062, 53.459
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-443-

HOH

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Components

#1: Protein Minor nucleoprotein VP30


Mass: 16747.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengla dianlovirus / Gene: VP30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A3S8UVN5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Sulfate , 0.1M Sodium, Acetate pH4.6, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.34→40.87 Å / Num. obs: 36367 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.06541 / Rpim(I) all: 0.03027 / Rrim(I) all: 0.07254 / Net I/σ(I): 16.27
Reflection shellResolution: 1.344→1.392 Å / Rmerge(I) obs: 0.4376 / Mean I/σ(I) obs: 2.82 / Num. unique obs: 3598 / CC1/2: 0.852 / CC star: 0.959 / Rpim(I) all: 0.2158 / Rrim(I) all: 0.4909

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T3W

5t3w


Resolution: 1.34→40.87 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.185 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15496 1792 4.9 %RANDOM
Rwork0.12705 ---
obs0.12848 34575 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.282 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0.25 Å2-0 Å2
2---0.5 Å20 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 1.34→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 11 152 1171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191104
X-RAY DIFFRACTIONr_bond_other_d0.0010.021018
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.8881515
X-RAY DIFFRACTIONr_angle_other_deg1.2882.9252381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7655150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22825.20848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73715200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.829156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021251
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02211
X-RAY DIFFRACTIONr_mcbond_it2.2461.838552
X-RAY DIFFRACTIONr_mcbond_other1.9941.826551
X-RAY DIFFRACTIONr_mcangle_it2.4722.757700
X-RAY DIFFRACTIONr_mcangle_other2.4882.768701
X-RAY DIFFRACTIONr_scbond_it9.9822.555552
X-RAY DIFFRACTIONr_scbond_other9.9272.555549
X-RAY DIFFRACTIONr_scangle_other9.1813.573804
X-RAY DIFFRACTIONr_long_range_B_refined5.00325.0111357
X-RAY DIFFRACTIONr_long_range_B_other4.53224.1991319
X-RAY DIFFRACTIONr_rigid_bond_restr6.1432120
LS refinement shellResolution: 1.344→1.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 117 -
Rwork0.275 2542 -
obs--98.92 %

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