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- PDB-4ncc: Neutralizing antibody to murine norovirus -

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Basic information

Entry
Database: PDB / ID: 4ncc
TitleNeutralizing antibody to murine norovirus
Components
  • Fab fragment heavy
  • Fab fragment light
KeywordsIMMUNE SYSTEM / Immunoglobin / antibody / murine norovirus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSmith, T. / Li, M.
CitationJournal: J.Virol. / Year: 2014
Title: Flexibility in surface-exposed loops in a virus capsid mediates escape from antibody neutralization.
Authors: Kolawole, A.O. / Li, M. / Xia, C. / Fischer, A.E. / Giacobbi, N.S. / Rippinger, C.M. / Proescher, J.B. / Wu, S.K. / Bessling, S.L. / Gamez, M. / Yu, C. / Zhang, R. / Mehoke, T.S. / Pipas, J. ...Authors: Kolawole, A.O. / Li, M. / Xia, C. / Fischer, A.E. / Giacobbi, N.S. / Rippinger, C.M. / Proescher, J.B. / Wu, S.K. / Bessling, S.L. / Gamez, M. / Yu, C. / Zhang, R. / Mehoke, T.S. / Pipas, J.M. / Wolfe, J.T. / Lin, J.S. / Feldman, A.B. / Smith, T.J. / Wobus, C.E.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab fragment light
H: Fab fragment heavy
1: Fab fragment light
2: Fab fragment heavy


Theoretical massNumber of molelcules
Total (without water)93,6854
Polymers93,6854
Non-polymers00
Water6,666370
1
L: Fab fragment light
H: Fab fragment heavy


Theoretical massNumber of molelcules
Total (without water)46,8432
Polymers46,8432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-20 kcal/mol
Surface area19590 Å2
MethodPISA
2
1: Fab fragment light
2: Fab fragment heavy


Theoretical massNumber of molelcules
Total (without water)46,8432
Polymers46,8432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-21 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.590, 135.810, 83.310
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111Chain L and resid 1:106
211Chain 1 and resid 1:106
112Chain L and resid 107:210
212Chain 1 and resid 107:210
113Chain H and resid 2:119
213Chain 2 and resid 2:119
114Chain H and resid 120:221
214Chain 2 and resid 120:221

NCS ensembles :
ID
1
2
3
4
DetailsThere are two Fabs in the asymmetric unit. L (light) and H (heavy) chains make one and chains 1 and 2 make the other where 1=light and 2=heavy

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Components

#1: Antibody Fab fragment light


Mass: 23083.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab fragment heavy


Mass: 23759.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 298 K / pH: 7.6
Details: Protein concentration 9.7 mg/ml in 50mM Tris. Reservoir 18% PEG 8000 in 90 mM Tris, pH 8.5. Drop was 5 microliters of reservoir and 5 of protein., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 1, 2013
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→42.49 Å / Num. obs: 20909 / % possible obs: 63 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
SAINTdata reduction
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→42.49 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 0 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 1138 4.83 %
Rwork0.204 --
obs0.207 20909 71.4 %
all-23539 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.96 Å2
Refinement stepCycle: LAST / Resolution: 2.49→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 0 370 6930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116738
X-RAY DIFFRACTIONf_angle_d1.4749168
X-RAY DIFFRACTIONf_dihedral_angle_d15.7892394
X-RAY DIFFRACTIONf_chiral_restr0.1041028
X-RAY DIFFRACTIONf_plane_restr0.0061158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L786X-RAY DIFFRACTIONPOSITIONAL
121786X-RAY DIFFRACTIONPOSITIONAL0.063
21L814X-RAY DIFFRACTIONPOSITIONAL
221814X-RAY DIFFRACTIONPOSITIONAL0.114
31H933X-RAY DIFFRACTIONPOSITIONAL
322933X-RAY DIFFRACTIONPOSITIONAL0.081
41H731X-RAY DIFFRACTIONPOSITIONAL
422731X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4923-2.60580.3014490.20571128X-RAY DIFFRACTION29
2.6058-2.74310.3162990.22461711X-RAY DIFFRACTION44
2.7431-2.91490.33851420.22672685X-RAY DIFFRACTION69
2.9149-3.13990.30171710.2483189X-RAY DIFFRACTION82
3.1399-3.45580.33951660.2293407X-RAY DIFFRACTION87
3.4558-3.95550.27071580.20913384X-RAY DIFFRACTION86
3.9555-4.98230.21481720.15843498X-RAY DIFFRACTION89
4.9823-42.4960.21291810.18153399X-RAY DIFFRACTION86

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