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- PDB-4rdj: Crystal structure of Norovirus Boxer P domain -

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Basic information

Entry
Database: PDB / ID: 4rdj
TitleCrystal structure of Norovirus Boxer P domain
ComponentsCapsid
KeywordsVIRAL PROTEIN / mixed alpha/beta structure / virus capsid / receptor binding / HBGA
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman calicivirus NLV/Boxer/2001/US
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHao, N. / Chen, Y. / Xia, M. / Liu, W. / Tan, M. / Jiang, X. / Li, X.
CitationJournal: Protein Cell / Year: 2015
Title: Crystal structures of GI.8 Boxer virus P dimers in complex with HBGAs, a novel evolutionary path selected by the Lewis epitope.
Authors: Hao, N. / Chen, Y. / Xia, M. / Tan, M. / Liu, W. / Guan, X. / Jiang, X. / Li, X. / Rao, Z.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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
B: Capsid


Theoretical massNumber of molelcules
Total (without water)67,5182
Polymers67,5182
Non-polymers00
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-28 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.867, 139.867, 64.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Capsid


Mass: 33758.879 Da / Num. of mol.: 2 / Fragment: Protrusion domain, UNP residues 227-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human calicivirus NLV/Boxer/2001/US / Plasmid: pGex-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8BCA3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M LiCl, 18% (w/v) PEG 3350, 10% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 115571 / Num. obs: 115571 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 42.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 11 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZL7

2zl7


Resolution: 1.5→29.377 Å / SU ML: 0.15 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1627 5825 5.05 %RANDOM
Rwork0.1362 ---
obs0.1375 115416 99.99 %-
all-115416 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.44 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.3383 Å2-0 Å2-0 Å2
2--1.3383 Å2-0 Å2
3----2.6767 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 0 764 5316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064714
X-RAY DIFFRACTIONf_angle_d1.0576458
X-RAY DIFFRACTIONf_dihedral_angle_d12.321708
X-RAY DIFFRACTIONf_chiral_restr0.074710
X-RAY DIFFRACTIONf_plane_restr0.005864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.5-1.5170.21471960.14653637
1.517-1.53490.20542150.13743607
1.5349-1.55360.19611980.13763672
1.5536-1.57330.19711840.13743631
1.5733-1.5940.17912010.13413625
1.594-1.61580.1721950.13283629
1.6158-1.63890.17561950.12453656
1.6389-1.66340.1821930.12723589
1.6634-1.68930.15032110.12023620
1.6893-1.7170.16262000.11643668
1.717-1.74660.16841890.11623620
1.7466-1.77840.15551680.11163655
1.7784-1.81260.17291880.11163657
1.8126-1.84960.15931900.1173655
1.8496-1.88980.14692040.11563628
1.8898-1.93370.15622000.11853613
1.9337-1.98210.15591880.11713674
1.9821-2.03570.15471960.12243605
2.0357-2.09560.13261870.12193680
2.0956-2.16320.15422020.12733671
2.1632-2.24050.17491990.12853625
2.2405-2.33010.14421980.12533659
2.3301-2.43610.14781770.12683652
2.4361-2.56450.15221860.13853684
2.5645-2.72510.18281990.14893660
2.7251-2.93530.16841830.14393669
2.9353-3.23040.17541810.14583720
3.2304-3.6970.16891980.14483658
3.697-4.65490.1281950.13243712
4.6549-29.38250.18672090.17963760

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