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- PDB-7mu4: Crystal Structure of HPV L1-directed D24.M01Fab -

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Basic information

Entry
Database: PDB / ID: 7mu4
TitleCrystal Structure of HPV L1-directed D24.M01Fab
Components
  • D24.M01 Fab Heavy Chain
  • D24.M01 Fab Light Chain
KeywordsIMMUNE SYSTEM / Antigen Binding Fragment (Fab)
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 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
Revision 1.2Oct 16, 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: D24.M01 Fab Heavy Chain
L: D24.M01 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7633
Polymers54,6562
Non-polymers1061
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-23 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.021, 77.743, 105.029
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

#1: Antibody D24.M01 Fab Heavy Chain


Mass: 29735.682 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 D24.M01 Fab Light Chain


Mass: 24920.762 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 10% w/v Polyethylene glycol 6000, 5% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→46.63 Å / Num. obs: 33966 / % possible obs: 89 % / Redundancy: 5.8 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.99 / Net I/σ(I): 19.9
Reflection shellResolution: 1.83→1.9 Å / Num. unique obs: 1715 / CC1/2: 0.714

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6APB

6apb


Resolution: 1.83→46.62 Å / SU ML: 0.1776 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2114 1723 5.08 %
Rwork0.1737 32179 -
obs0.1757 33902 89.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.41 Å2
Refinement stepCycle: LAST / Resolution: 1.83→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 7 312 3605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01133372
X-RAY DIFFRACTIONf_angle_d1.22954607
X-RAY DIFFRACTIONf_chiral_restr0.0613536
X-RAY DIFFRACTIONf_plane_restr0.008583
X-RAY DIFFRACTIONf_dihedral_angle_d19.6477472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.890.363680.2821267X-RAY DIFFRACTION43.26
1.89-1.950.2621060.22011870X-RAY DIFFRACTION62.59
1.95-2.020.21821000.19422192X-RAY DIFFRACTION73.79
2.02-2.10.21051400.17732605X-RAY DIFFRACTION87.45
2.1-2.190.22731780.17242927X-RAY DIFFRACTION99.3
2.19-2.310.2361440.16853001X-RAY DIFFRACTION100
2.31-2.450.21271400.17273017X-RAY DIFFRACTION100
2.46-2.640.22541790.17972985X-RAY DIFFRACTION100
2.64-2.910.21471690.17853020X-RAY DIFFRACTION99.94
2.91-3.330.21931610.16973025X-RAY DIFFRACTION99.91
3.33-4.20.17941500.15143080X-RAY DIFFRACTION99.97
4.2-46.620.20371880.18043190X-RAY DIFFRACTION99.68

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