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- PDB-4qhl: I3.2 (unbound) from CH103 Lineage -

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Basic information

Entry
Database: PDB / ID: 4qhl
TitleI3.2 (unbound) from CH103 Lineage
Components
  • I3 heavy chain
  • UCA light chain
KeywordsIMMUNE SYSTEM / Fab fragment / HIV-1 / antibody
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.153 Å
AuthorsFera, D. / Harrison, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains.
Authors: Fera, D. / Schmidt, A.G. / Haynes, B.F. / Gao, F. / Liao, H.X. / Kepler, T.B. / Harrison, S.C.
History
DepositionMay 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: I3 heavy chain
B: UCA light chain
C: I3 heavy chain
D: UCA light chain


Theoretical massNumber of molelcules
Total (without water)95,3584
Polymers95,3584
Non-polymers00
Water0
1
A: I3 heavy chain
B: UCA light chain


Theoretical massNumber of molelcules
Total (without water)47,6792
Polymers47,6792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-26 kcal/mol
Surface area19860 Å2
MethodPISA
2
C: I3 heavy chain
D: UCA light chain


Theoretical massNumber of molelcules
Total (without water)47,6792
Polymers47,6792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-25 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.078, 99.135, 163.318
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 I3 heavy chain


Mass: 24894.764 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293T / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6*PLUS
#2: Antibody UCA light chain


Mass: 22784.156 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293T / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)

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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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 2 M ammonium sulfate, 5% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2013
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 20862 / Num. obs: 20709 / % possible obs: 99 % / Redundancy: 2.2 % / Biso Wilson estimate: 48.67 Å2 / Rmerge(I) obs: 0.123 / Χ2: 1.341 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.15-3.22.20.38619161.201198.1
3.2-3.262.20.36219091.126197.8
3.26-3.332.20.32618851.264197.2
3.33-3.392.20.26319341.275198.2
3.39-3.472.20.24518761.228197.5
3.47-3.552.20.20718921.268198.7
3.55-3.642.20.18419581.271198.4
3.64-3.732.20.17718901.319199
3.73-3.842.20.1619451.315199
3.84-3.972.20.13519641.339199.7
3.97-4.112.20.1219071.356199.6
4.11-4.272.20.10319501.424199.3
4.27-4.472.20.09119531.5071100
4.47-4.72.20.08819311.723199.5
4.7-52.30.0919311.87199.5
5-5.382.20.08919121.468199.3
5.38-5.932.20.08919441.28198.9
5.93-6.782.20.08419491.189199.5
6.78-8.542.30.05519341.2181100
8.54-502.30.03519651.126199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.71 Å49.57 Å
Translation3.71 Å49.57 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JAN

4jan


Resolution: 3.153→49.568 Å / FOM work R set: 0.7958 / SU ML: 0.36 / σ(F): 1.36 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2815 1060 5.12 %
Rwork0.2366 --
obs0.2389 20706 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.42 Å2 / Biso mean: 59.58 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.153→49.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6458 0 0 0 6458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036627
X-RAY DIFFRACTIONf_angle_d0.7879046
X-RAY DIFFRACTIONf_chiral_restr0.0551035
X-RAY DIFFRACTIONf_plane_restr0.0031153
X-RAY DIFFRACTIONf_dihedral_angle_d12.2242328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.153-3.29610.36481240.34162374249897
3.2961-3.46990.32951290.29312389251899
3.4699-3.68720.31741290.25952413254299
3.6872-3.97180.3481200.264624592579100
3.9718-4.37130.27071580.211924142572100
4.3713-5.00330.19931340.181424612595100
5.0033-6.30160.26441270.214325052632100
6.3016-49.57360.25521390.219326312770100
Refinement TLS params.Method: refined / Origin x: 1.2021 Å / Origin y: -39.6461 Å / Origin z: 34.1755 Å
111213212223313233
T0.3068 Å2-0.0211 Å20.0377 Å2-0.2623 Å20.0286 Å2--0.3204 Å2
L0.4995 °2-0.2777 °20.6522 °2-0.0951 °2-0.3252 °2--1.0219 °2
S-0.0208 Å °0.0126 Å °0.005 Å °0.0193 Å °0.0116 Å °-0.0315 Å °-0.0646 Å °0.0149 Å °0.0353 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 215
2X-RAY DIFFRACTION1allB2 - 209
3X-RAY DIFFRACTION1allC1 - 215
4X-RAY DIFFRACTION1allD2 - 209

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