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- PDB-7er1: Crystal structure of capsid P domain of norovirus GI.3 VA115 comp... -

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Basic information

Entry
Database: PDB / ID: 7er1
TitleCrystal structure of capsid P domain of norovirus GI.3 VA115 complexed with Gala1-3Galb1-4Glc
Componentscapsid P domain
KeywordsVIRAL PROTEIN / histo-blood group antigens / human norovirus / viral receptor
Biological speciesNorovirus GI.3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFC0840300 China
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 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 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 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: capsid P domain
B: capsid P domain
C: capsid P domain
D: capsid P domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,5215
Polymers141,1784
Non-polymers3421
Water13,529751
1
A: capsid P domain
D: capsid P domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9323
Polymers70,5892
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-12 kcal/mol
Surface area23000 Å2
MethodPISA
2
B: capsid P domain
C: capsid P domain


Theoretical massNumber of molelcules
Total (without water)70,5892
Polymers70,5892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-15 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.290, 59.637, 91.419
Angle α, β, γ (deg.)102.280, 96.720, 109.770
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 231 - 533 / Label seq-ID: 13 - 315

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
capsid P domain


Mass: 35294.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GI.3 / Variant: VA115 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.2M Sodium formate pH 6.4, 17% (w/v) Polyethylene glycol 3350

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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: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 52013 / % possible obs: 94.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.042 / Rrim(I) all: 0.092 / Χ2: 0.97 / Net I/σ(I): 11 / Num. measured all: 236380
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.60.16119990.9780.0910.1860.6173.4
2.24-2.283.70.17924200.9740.1010.2060.68288
2.28-2.3240.17425530.9770.0950.1990.66692.3
2.32-2.374.20.16925720.980.090.1920.76193.8
2.37-2.424.40.16525720.980.0880.1880.74794.2
2.42-2.484.50.16626440.9790.0880.1880.76594.6
2.48-2.544.50.15425890.9830.0810.1740.87494.8
2.54-2.614.60.14226610.9850.0740.160.91995
2.61-2.694.60.13225980.9880.0690.1490.96895
2.69-2.774.60.12526090.9870.0660.1421.09595.8
2.77-2.874.70.11526250.9880.0610.131.14996
2.87-2.994.70.10926820.9870.0570.1231.15796.2
2.99-3.124.70.09826460.9890.0510.111.1696.5
3.12-3.294.80.0926420.990.0470.1021.1696.6
3.29-3.494.80.08126810.9920.0420.0921.11497.1
3.49-3.764.80.07627050.9930.040.0861.06797.7
3.76-4.144.80.07126660.9940.0370.0811.03997.7
4.14-4.744.90.06427060.9940.0330.0721.10398.2
4.74-5.974.90.0627300.9950.0310.0670.99698.7
5.97-504.80.04727130.9970.0240.0530.94199

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ER0

7er0


Resolution: 2.2→41.29 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.64 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 2621 5 %RANDOM
Rwork0.1781 ---
obs0.1802 49385 93.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.08 Å2 / Biso mean: 24.354 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å2-0.7 Å2-3.22 Å2
2---0.79 Å2-0.67 Å2
3---1.13 Å2
Refinement stepCycle: final / Resolution: 2.2→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9203 0 23 751 9977
Biso mean--59.99 28.27 -
Num. residues----1206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178350
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.64912987
X-RAY DIFFRACTIONr_angle_other_deg1.1491.56419496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56751199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48323.16462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.832151355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0251540
X-RAY DIFFRACTIONr_chiral_restr0.050.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021939
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A90060.1
12B90060.1
21A91180.07
22C91180.07
31A89340.09
32D89340.09
41B90850.08
42C90850.08
51B90080.08
52D90080.08
61C89210.09
62D89210.09
LS refinement shellResolution: 2.2→2.252 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.256 124 -
Rwork0.212 2549 -
obs--64.77 %

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