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- PDB-7mf7: Crystal structure of antibody 10E8v4-P100gA Fab -

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Basic information

Entry
Database: PDB / ID: 7mf7
TitleCrystal structure of antibody 10E8v4-P100gA Fab
Components
  • Antibody 10E8v4 Fab heavy chain
  • Antibody 10E8v4 Fab light chain
KeywordsIMMUNE SYSTEM / Monoclonal antibody 10E8 / MPER / cis-trans isomerization / size-exclusion chromatography
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKwon, Y.D. / Kwong, P.D.
CitationJournal: Antibodies / Year: 2021
Title: Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography.
Authors: Do Kwon, Y. / Wang, X.E. / Bender, M.F. / Yang, R. / Li, Y. / McKee, K. / Rawi, R. / O'Dell, S. / Schneck, N.A. / Shaddeau, A. / Zhang, B. / Arnold, F.J. / Connors, M. / Doria-Rose, N.A. / ...Authors: Do Kwon, Y. / Wang, X.E. / Bender, M.F. / Yang, R. / Li, Y. / McKee, K. / Rawi, R. / O'Dell, S. / Schneck, N.A. / Shaddeau, A. / Zhang, B. / Arnold, F.J. / Connors, M. / Doria-Rose, N.A. / Kwong, P.D. / Lei, Q.P.
History
DepositionApr 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Antibody 10E8v4 Fab heavy chain
L: Antibody 10E8v4 Fab light chain
A: Antibody 10E8v4 Fab heavy chain
B: Antibody 10E8v4 Fab light chain
C: Antibody 10E8v4 Fab heavy chain
D: Antibody 10E8v4 Fab light chain
E: Antibody 10E8v4 Fab heavy chain
F: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)192,2508
Polymers192,2508
Non-polymers00
Water12,142674
1
H: Antibody 10E8v4 Fab heavy chain
L: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0622
Polymers48,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-20 kcal/mol
Surface area20100 Å2
MethodPISA
2
A: Antibody 10E8v4 Fab heavy chain
B: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0622
Polymers48,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-21 kcal/mol
Surface area20340 Å2
MethodPISA
3
C: Antibody 10E8v4 Fab heavy chain
D: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0622
Polymers48,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-20 kcal/mol
Surface area20650 Å2
MethodPISA
4
E: Antibody 10E8v4 Fab heavy chain
F: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0622
Polymers48,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-19 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.216, 43.555, 226.462
Angle α, β, γ (deg.)90.000, 115.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
Antibody 10E8v4 Fab heavy chain


Mass: 25111.965 Da / Num. of mol.: 4 / Mutation: P100gA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-15*05 / Plasmid: pVRC8400 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody
Antibody 10E8v4 Fab light chain


Mass: 22950.463 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV3-19*01 / Plasmid: pVRC8400 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 8000, 1M Tris-HCl 8.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 12, 2019
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 127970 / % possible obs: 97.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 40.99 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.046 / Rrim(I) all: 0.104 / Χ2: 0.909 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.01-2.043.70.86158200.4860.4920.9970.6389.4
2.04-2.084.50.82463550.5720.4320.9350.69696.5
2.08-2.124.90.7663570.6020.3820.8550.73699.5
2.12-2.175.20.70664910.6780.3450.790.77898.7
2.17-2.215.40.64364540.7250.3050.7150.81299.5
2.21-2.265.60.58664740.7580.2720.6490.85498.8
2.26-2.325.50.51964390.8050.2420.5760.86198.8
2.32-2.385.40.45964300.840.2160.510.90498.9
2.38-2.455.30.3964830.8420.1880.4360.98698.8
2.45-2.5350.32661530.8880.1610.3661.04594.4
2.53-2.625.10.28162510.9110.1390.3161.08895.5
2.62-2.735.60.23165330.9460.110.2571.13199.2
2.73-2.855.60.18664610.9630.0880.2071.13799.1
2.85-35.50.14964720.9750.0720.1661.10998.7
3-3.195.30.11264780.9830.0560.1261.0698.6
3.19-3.445.10.08764570.9880.0450.0990.9997.6
3.44-3.784.70.07160980.990.0370.0810.90892
3.78-4.335.30.06465960.9940.0310.0720.82398.9
4.33-5.454.90.05865930.9950.0290.0660.74998.7
5.45-504.20.04965750.9960.0270.0560.62194.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IQ9

5iq9


Resolution: 2→36.47 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 2007 1.57 %
Rwork0.2027 125941 -
obs0.2031 127948 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.94 Å2 / Biso mean: 52.0205 Å2 / Biso min: 19.48 Å2
Refinement stepCycle: final / Resolution: 2→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13163 0 0 674 13837
Biso mean---52.77 -
Num. residues----1736
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.050.32481130.2917664972
2.05-2.10.29861400.2768905898
2.1-2.160.26041440.25925599
2.16-2.230.3111500.262918199
2.23-2.310.30511460.2617923099
2.31-2.410.30391400.2558922399
2.41-2.520.27211470.2468898797
2.52-2.650.27471430.2379892096
2.65-2.820.25071450.2333928599
2.82-3.030.24451510.2309928699
3.03-3.340.25751460.215921198
3.34-3.820.18911440.1849880594
3.82-4.810.18471500.1575945099
4.81-36.470.2161480.1744940196

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