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- PDB-4oov: Crystal structure of P domain from norovirus strain Farmington Hi... -

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Basic information

Entry
Database: PDB / ID: 4oov
TitleCrystal structure of P domain from norovirus strain Farmington Hills 2004
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / VIRAL 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
Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GII.4/Farmington Hills/2004/USA
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsSingh, B.K. / Leuthold, M. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Human noroviruses' fondness for histo-blood group antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / struct_ncs_dom_lim / 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_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 / _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: Major capsid protein
B: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,07010
Polymers67,5732
Non-polymers4978
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint7 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.950, 90.120, 109.210
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
Detailsbiological unit is the same as asym.

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Components

#1: Protein Major capsid protein


Mass: 33786.648 Da / Num. of mol.: 2 / Fragment: unp residues 225-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Farmington Hills/2004/USA
Gene: JQ478408 / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R4I4P2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 46.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97939 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.5→99.219 Å / Num. obs: 99095 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 12.14 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.941 / Net I/σ(I): 14.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.540.562.2727638707797
1.54-1.580.4713.1835308708399.6
1.58-1.630.4083.7834875688199.4
1.63-1.680.3384.5233451669699.7
1.68-1.730.2875.1531371649399.4
1.73-1.790.2266.3830517629099.4
1.79-1.860.1858.0331341607699.3
1.86-1.940.1649.2529680585599.3
1.94-2.020.12711.3827786559699.5
2.02-2.120.10213.2924869536599.1
2.12-2.240.08816.0926547512699.6
2.24-2.370.07718.524869487899.5
2.37-2.540.06620.4823272458599.6
2.54-2.740.05722.2119993427299.2
2.74-30.04827.7120736395699.5
3-3.360.03735.1418431358399.5
3.36-3.880.03239.5815127318599.3
3.88-4.750.02846.813375270599
4.75-6.710.0343.8910516214399.4
6.710.02846.225595125097.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→99.219 Å / FOM work R set: 0.9112 / SU ML: 0.11 / σ(F): 1.36 / Phase error: 15.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1709 4684 5 %
Rwork0.1448 --
obs0.1461 93719 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.84 Å2 / Biso mean: 15.8 Å2 / Biso min: 5.21 Å2
Refinement stepCycle: LAST / Resolution: 1.53→99.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 32 775 5543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094925
X-RAY DIFFRACTIONf_angle_d1.296731
X-RAY DIFFRACTIONf_chiral_restr0.055738
X-RAY DIFFRACTIONf_plane_restr0.007898
X-RAY DIFFRACTIONf_dihedral_angle_d12.2661753
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2810X-RAY DIFFRACTION5.229TORSIONAL
12B2810X-RAY DIFFRACTION5.229TORSIONAL
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 (%)
1.53-1.54740.25721530.20592915306899
1.5474-1.56560.21691560.193929543110100
1.5656-1.58470.23381530.185629333086100
1.5847-1.60470.22221550.18492937309299
1.6047-1.62590.20671530.17782914306799
1.6259-1.64810.19891550.174729633118100
1.6481-1.67170.1991540.163929223076100
1.6717-1.69660.19751550.159729503105100
1.6966-1.72320.19311540.16312929308399
1.7232-1.75140.21071550.16242949310499
1.7514-1.78160.20041540.15662927308199
1.7816-1.8140.19381550.15392943309899
1.814-1.84890.20461570.1462979313699
1.8489-1.88660.17121540.15042940309499
1.8866-1.92770.18631540.1452918307299
1.9277-1.97250.16271560.14042961311799
1.9725-2.02180.16871540.131829483102100
2.0218-2.07650.16541550.13182945310099
2.0765-2.13760.1481550.13032945310099
2.1376-2.20660.14871580.129829943152100
2.2066-2.28550.14151560.12312963311999
2.2855-2.3770.15011560.128429573113100
2.377-2.48510.17331570.130929853142100
2.4851-2.61610.16361580.137330123170100
2.6161-2.780.15851560.14042957311399
2.78-2.99460.14891580.14530103168100
2.9946-3.29590.17561590.14233018317799
3.2959-3.77270.17711590.14393031319099
3.7727-4.75250.12871600.12943043320399
4.7525-46.72290.17851700.16023193336399

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