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- PDB-6vkx: Crystal structure of the carbohydrate-binding domain VP8* of huma... -

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Basic information

Entry
Database: PDB / ID: 6vkx
TitleCrystal structure of the carbohydrate-binding domain VP8* of human P[8] rotavirus strain BM13851
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / Rotavirus / host receptor interaction
Function / homologyHaemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / viral capsid / Concanavalin A-like lectin/glucanase domain superfamily / symbiont entry into host cell / virion attachment to host cell / DI(HYDROXYETHYL)ETHER / Outer capsid protein VP4 / Outer capsid protein VP4
Function and homology information
Biological speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsXu, S. / McGinnis, K.R. / Jiang, X. / Kennedy, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens.
Authors: Xu, S. / McGinnis, K.R. / Liu, Y. / Huang, P. / Tan, M. / Stuckert, M.R. / Burnside, R.E. / Jacob, E.G. / Ni, S. / Jiang, X. / Kennedy, M.A.
History
DepositionJan 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 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: Outer capsid protein VP4
B: Outer capsid protein VP4
C: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6136
Polymers55,2073
Non-polymers4063
Water2,108117
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7033
Polymers18,4021
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5082
Polymers18,4021
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,4021
Polymers18,4021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.999, 63.248, 71.941
Angle α, β, γ (deg.)90.000, 90.700, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer capsid protein VP4


Mass: 18402.191 Da / Num. of mol.: 3 / Fragment: VP8* domain, residues 17-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Gene: VP8 / Production host: Escherichia coli (E. coli) / References: UniProt: M4VSS2, UniProt: A0A1Z1XCF6*PLUS
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.31 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES sodium pH 7.5, 2% v/v PEG 400, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.71→56 Å / Num. obs: 48913 / % possible obs: 90 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.065 / Net I/σ(I): 12.7 / Num. measured all: 159999 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.71-1.83.40.4642598676830.7990.2940.5512.497.4
5.41-563.20.025556717130.9990.0160.02931.496.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NIW

6niw


Resolution: 1.71→32.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.687 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2380 4.9 %RANDOM
Rwork0.1978 ---
obs0.1993 46518 89.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.36 Å2 / Biso mean: 21.764 Å2 / Biso min: 11.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0.4 Å2
2--0.09 Å2-0 Å2
3---0.9 Å2
Refinement stepCycle: final / Resolution: 1.71→32.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 27 117 3956
Biso mean--40.27 24.64 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133940
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183345
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.6575361
X-RAY DIFFRACTIONr_angle_other_deg1.3551.5827783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8015465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37922.757243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35315595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8981526
X-RAY DIFFRACTIONr_chiral_restr0.0620.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02892
LS refinement shellResolution: 1.71→1.754 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 197 -
Rwork0.276 3677 -
all-3874 -
obs--97.53 %

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