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- PDB-5ca6: Crystallographic structure of apo porcine rotavirus TFR-41 VP8* -

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Basic information

Entry
Database: PDB / ID: 5ca6
TitleCrystallographic structure of apo porcine rotavirus TFR-41 VP8*
Componentsporcine rotavirus TFR-41 VP8*
Keywordsviral protein / sugar binding protein / carbohydrate-recognizing protein / lectin / rotavirus
Function / homology
Function and homology information


viral life cycle / viral capsid
Similarity search - Function
Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / PALMITIC ACID / VACCENIC ACID / Outer capsid protein VP4
Similarity search - Component
Biological speciesPorcine rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYu, X. / Blanchard, H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1085596 Australia
CitationJournal: Chembiochem / Year: 2015
Title: Substantial Receptor-induced Structural Rearrangement of Rotavirus VP8*: Potential Implications for Cross-Species Infection.
Authors: Yu, X. / Mishra, R. / Holloway, G. / von Itzstein, M. / Coulson, B.S. / Blanchard, H.
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: porcine rotavirus TFR-41 VP8*
B: porcine rotavirus TFR-41 VP8*
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,58014
Polymers36,3042
Non-polymers1,27612
Water5,981332
1
A: porcine rotavirus TFR-41 VP8*
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8238
Polymers18,1521
Non-polymers6717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: porcine rotavirus TFR-41 VP8*
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7576
Polymers18,1521
Non-polymers6055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.816, 30.444, 86.217
Angle α, β, γ (deg.)90.00, 124.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

21B-568-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein porcine rotavirus TFR-41 VP8*


Mass: 18152.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine rotavirus (serotype 5 / strain TFR-41)
Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1A9TAH8*PLUS

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Non-polymers , 5 types, 344 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.4 and 2 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.9→42.91 Å / Num. obs: 23031 / % possible obs: 98.4 % / Redundancy: 5.4 % / Net I/σ(I): 13
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.148 / Num. unique all: 2985 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I2S

2i2s


Resolution: 1.9→35.8 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.107 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20254 1170 5.1 %RANDOM
Rwork0.16426 ---
obs0.16616 21861 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.564 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.08 Å2
2---0.53 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 86 336 2958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022736
X-RAY DIFFRACTIONr_bond_other_d0.0010.022504
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9543738
X-RAY DIFFRACTIONr_angle_other_deg0.72435784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3624.833120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.24115398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.622158
X-RAY DIFFRACTIONr_chiral_restr0.070.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5051.1261300
X-RAY DIFFRACTIONr_mcbond_other0.5051.1281301
X-RAY DIFFRACTIONr_mcangle_it0.8571.6821631
X-RAY DIFFRACTIONr_mcangle_other0.8581.6821632
X-RAY DIFFRACTIONr_scbond_it0.6541.2471436
X-RAY DIFFRACTIONr_scbond_other0.6541.2471437
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0681.8182103
X-RAY DIFFRACTIONr_long_range_B_refined4.19810.443268
X-RAY DIFFRACTIONr_long_range_B_other4.19710.4443269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 68 -
Rwork0.161 1340 -
obs--84.26 %

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