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- PDB-6wrp: Crystal Structure of PI3-E12 Fab, An Antibody Against Human Parai... -

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Basic information

Entry
Database: PDB / ID: 6wrp
TitleCrystal Structure of PI3-E12 Fab, An Antibody Against Human Parainfluenza Virus Type III
Components
  • PI3-E12 Fab Heavy Chain
  • PI3-E12 Fab Light Chain
KeywordsIMMUNE SYSTEM / antibody / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / AMMONIUM ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsWeidle, C. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Mabs / Year: 2021
Title: Protective antibodies against human parainfluenza virus type 3 infection.
Authors: Boonyaratanakornkit, J. / Singh, S. / Weidle, C. / Rodarte, J. / Bakthavatsalam, R. / Perkins, J. / Stewart-Jones, G.B.E. / Kwong, P.D. / McGuire, A.T. / Pancera, M. / Taylor, J.J.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: PI3-E12 Fab Heavy Chain
L: PI3-E12 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,50514
Polymers48,5362
Non-polymers96912
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, An SDS page gel was run on the purified Fab.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-56 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.031, 79.924, 99.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody PI3-E12 Fab Heavy Chain


Mass: 24763.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 293 / Production host: Homo sapiens (human)
#2: Antibody PI3-E12 Fab Light Chain


Mass: 23772.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 350 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2.2M Ammonium Sulfate, 2.2% PEG 400, 0.11M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 16, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 24469 / % possible obs: 98 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.41 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.01
Reflection shellResolution: 2.09→2.13 Å / Num. unique obs: 2026 / CC1/2: 0.905

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFT

6mft


Resolution: 2.08→23.79 Å / SU ML: 0.2547 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.3616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 1169 4.85 %
Rwork0.1961 22916 -
obs0.1988 24085 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.24 Å2
Refinement stepCycle: LAST / Resolution: 2.08→23.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 58 338 3688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023459
X-RAY DIFFRACTIONf_angle_d0.5114700
X-RAY DIFFRACTIONf_chiral_restr0.0428525
X-RAY DIFFRACTIONf_plane_restr0.0028601
X-RAY DIFFRACTIONf_dihedral_angle_d17.49711251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.170.32991210.22712463X-RAY DIFFRACTION84.28
2.17-2.290.34291250.28622720X-RAY DIFFRACTION91.54
2.29-2.430.36621490.23662847X-RAY DIFFRACTION95.87
2.43-2.620.30291350.23292896X-RAY DIFFRACTION98.41
2.62-2.880.27581610.22272929X-RAY DIFFRACTION98.85
2.88-3.30.25121580.19922952X-RAY DIFFRACTION99.08
3.3-4.150.20941540.162961X-RAY DIFFRACTION97.8
4.15-23.790.19741660.16563148X-RAY DIFFRACTION99.73

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