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- PDB-7rdj: Crystal structure of PCDN-16B, an anti-HIV antibody from the PCDN... -

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Basic information

Entry
Database: PDB / ID: 7rdj
TitleCrystal structure of PCDN-16B, an anti-HIV antibody from the PCDN bnAb lineage (non-cysteinylated state)
Components
  • PCDN-16B Fab heavy chain
  • PCDN-16B Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin / Broadly Neutralizing / HIV-1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsOmorodion, O. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
Bill & Melinda Gates FoundationOPP119635 United States
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural and Biochemical Characterization of Cysteinylation in Broadly Neutralizing Antibodies to HIV-1.
Authors: Omorodion, O. / Wilson, I.A.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 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
A: PCDN-16B Fab light chain
B: PCDN-16B Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,81810
Polymers48,2782
Non-polymers5418
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-3 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.796, 76.778, 62.423
Angle α, β, γ (deg.)90.000, 92.042, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody PCDN-16B Fab light chain


Mass: 23458.986 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 PCDN-16B Fab heavy chain


Mass: 24818.750 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M disodium tartrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 32727 / % possible obs: 98.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 22.34 Å2 / CC1/2: 0.8 / Rpim(I) all: 0.1 / Rsym value: 0.14 / Net I/σ(I): 7.4
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1649 / CC1/2: 0.43 / Rpim(I) all: 0.5 / Rsym value: 0.7 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-20002.3.10data reduction
SCALEPACKdata scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BZD

5bzd


Resolution: 1.93→48.42 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2103 1640 5.01 %
Rwork0.1701 31065 -
obs0.1723 32705 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.03 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 35 562 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323535
X-RAY DIFFRACTIONf_angle_d0.67564827
X-RAY DIFFRACTIONf_chiral_restr0.0455543
X-RAY DIFFRACTIONf_plane_restr0.0051620
X-RAY DIFFRACTIONf_dihedral_angle_d18.04261293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.32591300.25572309X-RAY DIFFRACTION87.96
1.98-2.050.27621540.2292575X-RAY DIFFRACTION98.38
2.05-2.120.2531220.21382602X-RAY DIFFRACTION98.48
2.12-2.210.27941400.20172592X-RAY DIFFRACTION98.06
2.21-2.310.23861180.19552620X-RAY DIFFRACTION99.02
2.31-2.430.25031090.19412635X-RAY DIFFRACTION99.1
2.43-2.580.31641210.19892610X-RAY DIFFRACTION98.24
2.58-2.780.24641350.19142609X-RAY DIFFRACTION98.74
2.78-3.060.22661400.16972637X-RAY DIFFRACTION99.25
3.06-3.50.1961520.15462598X-RAY DIFFRACTION98.81
3.5-4.410.15031380.12482639X-RAY DIFFRACTION98.97
4.41-48.420.161810.14312639X-RAY DIFFRACTION98.77

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