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- PDB-5itb: Crystal structure of the anti-RSV F Fab 14N4 -

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Basic information

Entry
Database: PDB / ID: 5itb
TitleCrystal structure of the anti-RSV F Fab 14N4
Components
  • anti-RSV F Fab 14N4 Heavy chain
  • anti-RSV F Fab 14N4 Light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMousa, J.J. / Crowe, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for nonneutralizing antibody competition at antigenic site II of the respiratory syncytial virus fusion protein.
Authors: Mousa, J.J. / Sauer, M.F. / Sevy, A.M. / Finn, J.A. / Bates, J.T. / Alvarado, G. / King, H.G. / Loerinc, L.B. / Fong, R.H. / Doranz, B.J. / Correia, B.E. / Kalyuzhniy, O. / Wen, X. / ...Authors: Mousa, J.J. / Sauer, M.F. / Sevy, A.M. / Finn, J.A. / Bates, J.T. / Alvarado, G. / King, H.G. / Loerinc, L.B. / Fong, R.H. / Doranz, B.J. / Correia, B.E. / Kalyuzhniy, O. / Wen, X. / Jardetzky, T.S. / Schief, W.R. / Ohi, M.D. / Meiler, J. / Crowe, J.E.
History
DepositionMar 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Refinement description / Category: citation / software / Item: _citation.journal_id_CSD
Revision 1.3Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: anti-RSV F Fab 14N4 Heavy chain
L: anti-RSV F Fab 14N4 Light chain


Theoretical massNumber of molelcules
Total (without water)46,8932
Polymers46,8932
Non-polymers00
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-29 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.447, 75.129, 61.374
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody anti-RSV F Fab 14N4 Heavy chain


Mass: 23128.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody anti-RSV F Fab 14N4 Light chain


Mass: 23764.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 50 mM zinc acetate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→28.36 Å / Num. obs: 27310 / % possible obs: 99.6 % / Redundancy: 4.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XPREPdata reduction
PHENIX(1.10.1_2155:000)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q9Q

4q9q


Resolution: 2→28.353 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 1396 5.12 %Random selection
Rwork0.1937 ---
obs0.1947 27288 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 0 416 3704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123360
X-RAY DIFFRACTIONf_angle_d1.3614562
X-RAY DIFFRACTIONf_dihedral_angle_d15.1651198
X-RAY DIFFRACTIONf_chiral_restr0.053520
X-RAY DIFFRACTIONf_plane_restr0.006572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.24751390.24312575X-RAY DIFFRACTION100
2.0715-2.15440.25181350.22962587X-RAY DIFFRACTION100
2.1544-2.25240.22231400.22372574X-RAY DIFFRACTION100
2.2524-2.37110.2671430.21622585X-RAY DIFFRACTION100
2.3711-2.51960.23981920.21282508X-RAY DIFFRACTION100
2.5196-2.7140.20551320.20992593X-RAY DIFFRACTION100
2.714-2.98680.2251590.20282576X-RAY DIFFRACTION100
2.9868-3.41840.19991230.17692614X-RAY DIFFRACTION100
3.4184-4.30440.19391070.16242617X-RAY DIFFRACTION100
4.3044-28.35620.16941260.17272663X-RAY DIFFRACTION100

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