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- PDB-5f4o: Protruding domain of GII.17 norovirus Kawasaki308 -

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Basic information

Entry
Database: PDB / ID: 5f4o
TitleProtruding domain of GII.17 norovirus Kawasaki308
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / Norovirus / Capsid protein / Protruding domain
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 Hu/GII/JP/2015/GII.P17_GII.17/Kawasaki308
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Structural Evolution of the Emerging 2014-2015 GII.17 Noroviruses.
Authors: Singh, B.K. / Koromyslova, A. / Hefele, L. / Gurth, C. / Hansman, G.S.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,12413
Polymers68,5162
Non-polymers60711
Water10,142563
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-6 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.720, 86.970, 97.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 224 - 530 / Label seq-ID: 1 - 307

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Capsid protein VP1 /


Mass: 34258.152 Da / Num. of mol.: 2 / Fragment: P DOMAIN (UNP residues 225-530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII/JP/2015/GII.P17_GII.17/Kawasaki308
Gene: VP1 / Plasmid: MBP-HTSHP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E4B1P1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Magnesium Chloride, PEG8000, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 13, 2015
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.58→43.485 Å / Num. obs: 85727 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 16.81 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.076 / Χ2: 0.971 / Net I/σ(I): 11.75 / Num. measured all: 333283
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.58-1.620.6580.7121.6822565647661760.82695.4
1.62-1.660.7610.5782.1323267632262560.66799
1.66-1.710.8510.4482.6321964618860670.51998
1.71-1.770.9230.323.7222711596757690.36796.7
1.77-1.820.9460.254.721532577855530.28696.1
1.82-1.890.9610.2145.6121612566254650.24496.5
1.89-1.960.9760.1677.0821595542753330.1998.3
1.96-2.040.9840.1348.7820729522151190.15398
2.04-2.130.9880.11410.319690502949250.12997.9
2.13-2.230.9920.09512.0618487480046820.10997.5
2.23-2.350.9940.07813.6116703459144550.0997
2.35-2.50.9960.07114.9916129434541630.08195.8
2.5-2.670.9960.06417.0514998408738200.07393.5
2.67-2.880.9970.05320.3114910383236610.06195.5
2.88-3.160.9980.04524.4213883352634070.05196.6
3.16-3.530.9980.03629.2912389320830770.04195.9
3.53-4.080.9990.0332.610577285427200.03595.3
4.08-4.990.9990.02734.188525244022820.03193.5
4.99-7.060.9990.0333.436930191217550.03491.8
7.060.9990.02636.674087114210420.0391.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.24 Å43.48 Å
Translation7.24 Å43.48 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F4M

5f4m


Resolution: 1.59→43.485 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.174 4207 5 %
Rwork0.1514 79922 -
obs0.1526 84129 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.16 Å2 / Biso mean: 23.4047 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 1.59→43.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4759 0 38 563 5360
Biso mean--29.13 28.33 -
Num. residues----610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084989
X-RAY DIFFRACTIONf_angle_d1.1896814
X-RAY DIFFRACTIONf_chiral_restr0.051729
X-RAY DIFFRACTIONf_plane_restr0.007918
X-RAY DIFFRACTIONf_dihedral_angle_d12.5921815
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3516X-RAY DIFFRACTION5.786TORSIONAL
12B3516X-RAY DIFFRACTION5.786TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.60810.28861410.2662684282599
1.6081-1.6270.26521420.24742693283599
1.627-1.64680.23851430.22862718286199
1.6468-1.66770.27191410.22542668280999
1.6677-1.68960.27671390.21682674281398
1.6896-1.71280.24511410.1992675281698
1.7128-1.73720.20491380.18722620275897
1.7372-1.76320.21441390.17882647278697
1.7632-1.79070.19971380.16882629276797
1.7907-1.82010.21271370.16612611274895
1.8201-1.85150.21861350.16142569270494
1.8515-1.88510.16581420.15312685282798
1.8851-1.92140.2081410.14682688282998
1.9214-1.96060.1431420.1382684282698
1.9606-2.00320.15551400.13682673281398
2.0032-2.04980.17221420.13782679282198
2.0498-2.10110.17021410.13992695283698
2.1011-2.15790.1881400.14292679281998
2.1579-2.22140.15711420.13522685282798
2.2214-2.29310.16711410.13542680282197
2.2931-2.37510.15841390.13622647278697
2.3751-2.47010.16231390.142645278496
2.4701-2.58260.18051370.14752599273695
2.5826-2.71870.18181360.14742578271492
2.7187-2.8890.17991400.15092658279897
2.889-3.1120.15131420.14792699284197
3.112-3.42510.17591420.14852694283696
3.4251-3.92040.15151410.14762670281195
3.9204-4.93820.13031400.12642668280894
4.9382-43.50120.18091460.15672728287492
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.01710.37450.15880.85790.39640.71810.0497-0.02940.0968-0.0178-0.10950.1349-0.0668-0.11770.07520.13050.01720.00140.1338-0.02430.160526.63224.3021-6.4266
21.1023-0.08840.01041.37670.58520.74330.02240.10870.1873-0.17-0.10480.1414-0.1595-0.15050.06790.1530.0386-0.02490.1479-0.0090.1623.25357.1993-16.3071
30.95490.15220.13791.05030.41431.3140.0917-0.27270.29660.1513-0.12020.0383-0.1631-0.0003-0.0020.1873-0.04470.02450.1856-0.08370.223637.242718.02247.5438
41.5537-0.1998-0.46561.2971-0.45991.60510.0535-0.1763-0.00170.0669-0.03980.0447-0.05380.0309-0.05670.124-0.0276-0.00910.13340.00350.141434.9085-8.14295.1564
51.47540.4257-0.52680.9405-0.6851.30850.05110.0222-0.0004-0.0337-0.0807-0.1433-0.01250.11960.05950.12640.00860.00760.13440.01120.154750.5029-5.189-7.2776
61.00320.12290.42551.6595-0.66051.00160.04120.08140.0652-0.051-0.0841-0.0531-0.02540.07910.04820.11310.02080.03410.12930.01120.103247.43742.6275-16.1188
71.0549-0.009-0.02641.2272-0.56430.84490.05960.1082-0.0626-0.1288-0.1006-0.07190.06660.11550.03650.14450.02640.01590.15360.0040.120349.7374-7.7845-16.4024
80.71090.07830.130.6192-0.22641.63330.0663-0.0912-0.13410.0104-0.0672-0.06440.08270.0251-0.00610.1117-0.0145-0.01260.12910.01850.153838.4476-15.0070.5928
92.35910.11450.70581.682-0.50312.11550.0981-0.3859-0.04450.258-0.00910.4364-0.1137-0.1717-0.04110.2165-0.05140.01240.27480.06150.23134.1778-14.944816.709
101.3321-0.7309-0.09841.7219-0.2811.86980.0742-0.0959-0.2009-0.0663-0.02820.30070.1553-0.0999-0.04390.1694-0.0626-0.0240.18370.05950.262133.516-21.33138.1753
111.6962-0.01580.93331.999-0.59192.6825-0.0818-0.3576-0.30140.17270.04710.06790.05880.0402-0.03720.1915-0.07030.01480.3010.09420.244836.5113-20.86217.2664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 224 through 347 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 348 through 422 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 423 through 530 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 224 through 247 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 248 through 319 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 320 through 347 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 348 through 422 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 423 through 464 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 465 through 484 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 485 through 513 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 514 through 530 )B0

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