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- PDB-7eqt: Crystal structure of capsid P domain of norovirus GI.3 DSV comple... -

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Basic information

Entry
Database: PDB / ID: 7eqt
TitleCrystal structure of capsid P domain of norovirus GI.3 DSV complexed with Gala1-3Galb1-4Glc
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / histo-blood group antigens / human norovirus / viral receptor
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Viral coat protein subunit / Capsid protein
Function and homology information
Biological speciesDesert Shield virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsChen, Y.
CitationJournal: J.Virol. / Year: 2022
Title: Structural Insight into Terminal Galactose Recognition by Two Non-HBGA Binding GI.3 Noroviruses.
Authors: Wang, C. / Kang, H. / Tan, M. / Cong, J. / Su, D. / Li, X. / Chen, Y.
History
DepositionMay 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 3, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 5, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_gene_src_variant / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.4Nov 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

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3043
Polymers70,8002
Non-polymers5041
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Elution volumn at about 10ml on Superdex75
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-11 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.628, 101.048, 104.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Capsid protein


Mass: 35399.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desert Shield virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q66418
#2: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15.5% (w/v) polyethylene glycol 3350, 0.2M Sodium tartrate dibasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 42161 / % possible obs: 98 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.038 / Rrim(I) all: 0.127 / Χ2: 0.885 / Net I/σ(I): 6 / Num. measured all: 445899
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.093.40.46517190.8250.2720.5440.45781.7
2.09-2.124.50.43818890.8790.2170.4930.50288.5
2.12-2.165.50.41119670.910.1850.4540.50993.7
2.16-2.216.80.46120600.9390.1830.4980.58197
2.21-2.268.50.3821010.9290.1350.4051.34599.3
2.26-2.3110.40.621140.9490.1950.6310.7799.9
2.31-2.3711.40.33321350.9730.1030.3490.541100
2.37-2.4311.60.29721200.980.0910.3110.577100
2.43-2.511.70.27821360.9810.0840.2910.593100
2.5-2.58120.23921160.9840.0720.250.633100
2.58-2.6812.10.22521530.9850.0670.2350.664100
2.68-2.7812.30.18121480.9920.0540.1890.745100
2.78-2.9112.30.15121320.9930.0440.1570.854100
2.91-3.0612.50.13621500.9950.040.1420.928100
3.06-3.2512.40.11421420.9960.0330.1191.065100
3.25-3.5112.50.09821620.9960.0290.1021.226100
3.51-3.8612.40.10321810.9970.030.1081.243100
3.86-4.4212.40.07721810.9970.0230.081.228100
4.42-5.5612.30.0722200.9980.0210.0731.162100
5.56-5011.60.06523350.990.020.0681.06299.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EQS

7eqs


Resolution: 2.05→32.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.579 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 2164 5.1 %RANDOM
Rwork0.1789 ---
obs0.1812 39868 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.41 Å2 / Biso mean: 24.664 Å2 / Biso min: 12.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å20 Å2
2--0.54 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 2.05→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 34 592 5240
Biso mean--36.57 33.93 -
Num. residues----602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134787
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174190
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.6516543
X-RAY DIFFRACTIONr_angle_other_deg1.1671.579792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6795599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79323.133233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49315692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4281520
X-RAY DIFFRACTIONr_chiral_restr0.050.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02973
LS refinement shellResolution: 2.05→2.1 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.247 127 -
Rwork0.227 2423 -
obs--81.89 %

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