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- PDB-7sd2: Murine Fab that recognizes Hev b 8 (profilin for Hevea brasiliensis) -

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Basic information

Entry
Database: PDB / ID: 7sd2
TitleMurine Fab that recognizes Hev b 8 (profilin for Hevea brasiliensis)
Components
  • Heavy Chain Antibody IgE/Fab anti-profilin Hev b 8
  • Light Chain Antibody IgE/Fab anti-profilin Hev b 8
KeywordsIMMUNE SYSTEM / Antibody / IgE/Fab fragment
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsRodriguez-Romero, A. / Garcia-Ramirez, B.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)087163 Mexico
Citation
Journal: Commun Biol / Year: 2022
Title: A native IgE in complex with profilin provides insights into allergen recognition and cross-reactivity.
Authors: Garcia-Ramirez, B. / Mares-Mejia, I. / Rodriguez-Hernandez, A. / Cano-Sanchez, P. / Torres-Larios, A. / Ortega, E. / Rodriguez-Romero, A.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2006
Title: HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes.
Authors: Minor, W. / Cymborowski, M. / Otwinowski, Z. / Chruszcz, M.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy Chain Antibody IgE/Fab anti-profilin Hev b 8
L: Light Chain Antibody IgE/Fab anti-profilin Hev b 8
A: Heavy Chain Antibody IgE/Fab anti-profilin Hev b 8
B: Light Chain Antibody IgE/Fab anti-profilin Hev b 8
C: Heavy Chain Antibody IgE/Fab anti-profilin Hev b 8
D: Light Chain Antibody IgE/Fab anti-profilin Hev b 8


Theoretical massNumber of molelcules
Total (without water)140,5276
Polymers140,5276
Non-polymers00
Water00
1
H: Heavy Chain Antibody IgE/Fab anti-profilin Hev b 8
L: Light Chain Antibody IgE/Fab anti-profilin Hev b 8


Theoretical massNumber of molelcules
Total (without water)46,8422
Polymers46,8422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-26 kcal/mol
Surface area18100 Å2
MethodPISA
2
A: Heavy Chain Antibody IgE/Fab anti-profilin Hev b 8
B: Light Chain Antibody IgE/Fab anti-profilin Hev b 8


Theoretical massNumber of molelcules
Total (without water)46,8422
Polymers46,8422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-25 kcal/mol
Surface area18070 Å2
MethodPISA
3
C: Heavy Chain Antibody IgE/Fab anti-profilin Hev b 8
D: Light Chain Antibody IgE/Fab anti-profilin Hev b 8


Theoretical massNumber of molelcules
Total (without water)46,8422
Polymers46,8422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-23 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.000, 103.845, 180.204
Angle α, β, γ (deg.)90.000, 94.258, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Antibody Heavy Chain Antibody IgE/Fab anti-profilin Hev b 8


Mass: 23226.309 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Light Chain Antibody IgE/Fab anti-profilin Hev b 8


Mass: 23616.020 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.2 M magnesium acetate tetrahydrate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.75→55.92 Å / Num. obs: 17207 / % possible obs: 99.09 % / Redundancy: 3.3 % / Biso Wilson estimate: 99.76 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.084 / Net I/σ(I): 8.1
Reflection shellResolution: 3.75→4.19 Å / Num. unique obs: 4862 / CC1/2: 0.843 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BAF

1baf


Resolution: 3.75→44.96 Å / SU ML: 0.4617 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.2298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2841 799 4.66 %
Rwork0.2465 16353 -
obs0.2484 17152 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.02 Å2
Refinement stepCycle: LAST / Resolution: 3.75→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 0 0 8148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00238361
X-RAY DIFFRACTIONf_angle_d0.556611534
X-RAY DIFFRACTIONf_chiral_restr0.04171319
X-RAY DIFFRACTIONf_plane_restr0.00511535
X-RAY DIFFRACTIONf_dihedral_angle_d4.08031304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.75-3.980.34251100.29322730X-RAY DIFFRACTION99.72
3.98-4.290.36991380.28242712X-RAY DIFFRACTION99.41
4.29-4.720.23381280.232689X-RAY DIFFRACTION98.29
4.72-5.410.28391470.23062714X-RAY DIFFRACTION99.76
5.41-6.810.31051240.26962765X-RAY DIFFRACTION99.72
6.81-44.960.25491520.22372743X-RAY DIFFRACTION98.07

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