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- PDB-7mx8: Crystal Structure of HPV L1-directed E7M03 Fab -

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Basic information

Entry
Database: PDB / ID: 7mx8
TitleCrystal Structure of HPV L1-directed E7M03 Fab
Components
  • E7M03 Fab Heavy Chain
  • E7M03 Fab Light Chain
KeywordsIMMUNE SYSTEM / Antigen Binding Fragment (Fab)
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsSingh, S. / Pancera, M.
CitationJournal: To Be Published
Title: Structural Characterisation of Immune Responses to HPV Vaccination
Authors: Singh, S. / Pancera, M. / Rodarte, J. / Carter, J.
History
DepositionMay 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 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: E7M03 Fab Heavy Chain
L: E7M03 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)55,6522
Polymers55,6522
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-27 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.716, 73.037, 125.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody E7M03 Fab Heavy Chain


Mass: 29742.613 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 E7M03 Fab Light Chain


Mass: 25908.916 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.: 128 / 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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.5M Ammonium Sulfate, 0.1 M tris(pH 8.5), 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 34084 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC1/2: 0.974 / Net I/σ(I): 15.7
Reflection shellResolution: 2.02→2.05 Å / Num. unique obs: 1659 / CC1/2: 0.956

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DRX

5drx


Resolution: 2.02→47.49 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1667 4.93 %
Rwork0.2083 32157 -
obs0.2101 33824 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.3 Å2 / Biso mean: 51.7191 Å2 / Biso min: 32.09 Å2
Refinement stepCycle: final / Resolution: 2.02→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 0 128 3456
Biso mean---52.67 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073433
X-RAY DIFFRACTIONf_angle_d0.9494689
X-RAY DIFFRACTIONf_dihedral_angle_d6.682481
X-RAY DIFFRACTIONf_chiral_restr0.056529
X-RAY DIFFRACTIONf_plane_restr0.006597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.02-2.080.37251270.3264260897
2.08-2.150.30261600.27442659100
2.15-2.230.34521300.25762634100
2.23-2.320.29851510.26592635100
2.32-2.420.28341390.2474265199
2.42-2.550.26881350.23042657100
2.55-2.710.27531420.23252660100
2.71-2.920.24561480.2379265499
2.92-3.210.27511420.23272700100
3.21-3.680.27541360.2115270199
3.68-4.630.21641220.1773274799
4.63-4.7490.18471350.1723285198

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