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- PDB-4opv: Unliganded crystal structure of P domain from norovirus strain Fa... -

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Basic information

Entry
Database: PDB / ID: 4opv
TitleUnliganded crystal structure of P domain from norovirus strain Farmington Hills 2004 co-crystallized with HBGA type Lea
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / Norovirus / Viral Capsid Protein / Histo Blood Group Antigen (HBGA) / Protruding Domain
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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...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 / 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: 1.85 Å
AuthorsSingh, B.K. / Leuthold, M.M. / Hansman, G.S.
CitationJournal: To be Published
Title: Unliganded crystal structure of P domain from norovirus strain Farmington Hills 2004 co-crystallized with HBGA type Lea
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionFeb 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)67,5732
Polymers67,5732
Non-polymers00
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-12 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.130, 90.150, 109.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Major capsid protein


Mass: 33786.648 Da / Num. of mol.: 2
Fragment: P domain Farmington Hills 2004 (residues 225 to 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.31 Å3/Da / Density % sol: 46.64 %
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: 0.93223 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93223 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 53177 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 15.73 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.94
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.85-1.90.423.52186.2
1.9-1.950.3264.95198.9
1.95-2.010.2646.35199
2.01-2.070.2057.88199.6
2.07-2.140.1719.22199.5
2.14-2.210.1510.37199.4
2.21-2.290.11912.82199.6
2.29-2.390.10814.18199.5
2.39-2.490.09915.37199.6
2.49-2.620.08317.87199.6
2.62-2.760.06920.73199.5
2.76-2.930.05425.28199.4
2.93-3.130.04131.9199.5
3.13-3.380.03140.67199.1
3.38-3.70.02546.22199.4
3.7-4.140.02351.77199
4.14-4.780.02156.87198.8
4.78-5.850.0253.19199.3
5.85-8.270.01952.52199.6
8.270.01362.72197.8

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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: 1.85→46.758 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 16.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1749 2658 5 %
Rwork0.1482 --
obs0.1495 53175 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.87 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 0 623 5355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064900
X-RAY DIFFRACTIONf_angle_d1.0786714
X-RAY DIFFRACTIONf_dihedral_angle_d12.3861746
X-RAY DIFFRACTIONf_chiral_restr0.043737
X-RAY DIFFRACTIONf_plane_restr0.006899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.88370.27631150.22582182X-RAY DIFFRACTION83
1.8837-1.920.21681370.20022619X-RAY DIFFRACTION96
1.92-1.95920.20371380.17452620X-RAY DIFFRACTION99
1.9592-2.00180.18441390.16362644X-RAY DIFFRACTION99
2.0018-2.04830.18741400.1542657X-RAY DIFFRACTION99
2.0483-2.09950.18891410.15282670X-RAY DIFFRACTION99
2.0995-2.15630.20391390.15332645X-RAY DIFFRACTION100
2.1563-2.21980.18241400.1442652X-RAY DIFFRACTION100
2.2198-2.29140.15791400.14142677X-RAY DIFFRACTION100
2.2914-2.37330.18191420.14162680X-RAY DIFFRACTION99
2.3733-2.46830.16861400.14142667X-RAY DIFFRACTION100
2.4683-2.58070.16341420.14482691X-RAY DIFFRACTION100
2.5807-2.71670.19671410.14392678X-RAY DIFFRACTION100
2.7167-2.88690.16771420.15082708X-RAY DIFFRACTION99
2.8869-3.10970.18391410.15052678X-RAY DIFFRACTION99
3.1097-3.42260.18121420.15012698X-RAY DIFFRACTION99
3.4226-3.91760.15871440.13832727X-RAY DIFFRACTION99
3.9176-4.9350.13491440.11892737X-RAY DIFFRACTION99
4.935-46.77280.16721510.15762887X-RAY DIFFRACTION99
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)
10.51140.47280.20071.63440.26560.8827-0.0357-0.01440.01230.02030.04660.05280.00330.0192-0.00690.07270.00670.00410.09160.01390.0689-16.1296-6.46524.6063
20.29160.0847-0.02461.2899-0.20150.8615-0.0105-0.04690.01520.0346-0.0121-0.03870.0620.06730.00530.0737-00.00160.09350.00810.0658-11.7838-12.12824.2435
31.1971-0.20180.00731.6430.49022.47680.00380.0726-0.0616-0.23090.0640.17090.2152-0.1142-0.05410.1803-0.0494-0.04990.11250.00930.1419-29.8553-25.17219.3942
41.5445-0.5281-0.58230.52590.07130.75790.0032-0.0001-0.0352-0.0192-0.00160.03940.04380.03190.00310.08-0.0105-0.01310.06310.00330.0619-19.30314.38756.4454
50.8319-0.8078-0.02921.6984-0.34320.8182-0.02470.02330.10280.02370.0049-0.1756-0.03050.11980.00250.0629-0.0202-0.00330.09850.01170.0813-6.11877.60016.5405
61.5291-0.4278-0.04680.6605-0.07450.4026-0.0244-0.0538-0.03610.05570.01990.0998-0.0356-0.04640.0050.09190.00650.00690.07730.00050.0562-35.228411.058514.5805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 224 through 352 )
2X-RAY DIFFRACTION2chain 'A' and (resid 353 through 464 )
3X-RAY DIFFRACTION3chain 'A' and (resid 465 through 530 )
4X-RAY DIFFRACTION4chain 'B' and (resid 225 through 323 )
5X-RAY DIFFRACTION5chain 'B' and (resid 324 through 419 )
6X-RAY DIFFRACTION6chain 'B' and (resid 420 through 530 )

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