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- PDB-4rlz: Crystal structure of Norovirus OIF P domain -

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Basic information

Entry
Database: PDB / ID: 4rlz
TitleCrystal structure of Norovirus OIF P domain
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / mixed alpha/beta structure / receptor binding / HBGA / virus caspid
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / 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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / 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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorovirus NLV/IF1998/2003/Iraq
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsLiu, W. / Chen, Y. / Tan, M. / Xia, M. / Li, X. / Jiang, X. / Rao, Z.
CitationJournal: Plos Pathog. / Year: 2015
Title: A Unique Human Norovirus Lineage with a Distinct HBGA Binding Interface.
Authors: Liu, W. / Chen, Y. / Jiang, X. / Xia, M. / Yang, Y. / Tan, M. / Li, X. / Rao, Z.
History
DepositionOct 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Experimental preparation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)69,0354
Polymers68,8512
Non-polymers1842
Water15,943885
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-19 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.495, 112.663, 59.711
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein / Capsid


Mass: 34425.258 Da / Num. of mol.: 2 / Fragment: Protrusion domain (UNP RESIDUES 220-527) / Mutation: H375N, H376I, S377A, Q378S, H379N, L387V, V389I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus NLV/IF1998/2003/Iraq / Strain: OIF / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6B7R3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 885 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 290 K / Method: liquid diffusion / pH: 6.5
Details: 0.1M Mes, pH6.5, 0.25M Ammonium Sulfate, 18% PEG 3350, LIQUID DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2012
RadiationMonochromator: Si(111) Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. all: 208854 / Num. obs: 197918 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.24
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 4.1 / Num. unique all: 8578 / % possible all: 86.9

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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: 3PUN

3pun


Resolution: 1.19→31.551 Å / SU ML: 0.12 / Isotropic thermal model: anisotropic / σ(F): 1.36 / Phase error: 14.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1595 9430 5.02 %RANDOM
Rwork0.1402 ---
all0.1412 197918 --
obs0.1412 187773 94.92 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.696 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso mean: 45.696 Å2
Baniso -1Baniso -2Baniso -3
1--1.3267 Å20 Å2-0.0269 Å2
2--0.5207 Å20 Å2
3---0.806 Å2
Refinement stepCycle: LAST / Resolution: 1.19→31.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4733 0 12 885 5630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054890
X-RAY DIFFRACTIONf_angle_d1.1316699
X-RAY DIFFRACTIONf_dihedral_angle_d12.4231761
X-RAY DIFFRACTIONf_chiral_restr0.075736
X-RAY DIFFRACTIONf_plane_restr0.005898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1899-1.20340.24522760.2109535286
1.2034-1.21760.22682890.1915578092
1.2176-1.23240.19892980.1772581193
1.2324-1.2480.20023160.167579593
1.248-1.26440.17722750.1564579092
1.2644-1.28170.16963230.1464575292
1.2817-1.30010.16083220.1403577092
1.3001-1.31950.16713260.1354567592
1.3195-1.34010.16313190.1292579092
1.3401-1.36210.15423050.1238571192
1.3621-1.38550.16412790.1228579192
1.3855-1.41070.15083120.1154583193
1.4107-1.43790.14652820.1105575693
1.4379-1.46720.13632980.1079586293
1.4672-1.49910.13633200.1091583193
1.4991-1.5340.13952940.1087586494
1.534-1.57240.14643130.1112592595
1.5724-1.61490.14673270.117596295
1.6149-1.66240.15713380.1192599196
1.6624-1.7160.15413350.1201601397
1.716-1.77740.14163320.1196612397
1.7774-1.84850.13022980.1236616098
1.8485-1.93260.15983360.1318617299
1.9326-2.03450.15133440.1338618899
2.0345-2.1620.16333570.13526246100
2.162-2.32880.1473330.13816215100
2.3288-2.56310.17492980.15386325100
2.5631-2.93370.16993450.15826277100
2.9337-3.69530.15413230.15346265100
3.6953-31.56220.16673170.1572632099

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