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- PDB-3qeg: Crystal structure of human N12-i2 Fab, an ADCC and neutralizing a... -

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Basic information

Entry
Database: PDB / ID: 3qeg
TitleCrystal structure of human N12-i2 Fab, an ADCC and neutralizing anti-HIV-1 Env antibody
Components
  • Fab fragment of human anti-HIV antibody N12-i2, heavy chain
  • Fab fragment of human anti-HIV antibody N12-i2, light chain
KeywordsIMMUNE SYSTEM / ADCC and neutralizing anti-HIV-1 Env antibody N12-i2 / CD4i antibody / Fab fragment / binds to viral glycoprotein gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGuan, Y. / DeVico, A.L. / Lewis, G.K. / Pazgier, M.
CitationJournal: To be Published
Title: Crystal structure of human N12-i2 Fab, an ADCC and neutralizing anti-HIV-1 Env antibody
Authors: Guan, Y. / DeVico, A.L. / Lewis, G.K. / Pazgier, M.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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
Revision 1.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab fragment of human anti-HIV antibody N12-i2, heavy chain
L: Fab fragment of human anti-HIV antibody N12-i2, light chain


Theoretical massNumber of molelcules
Total (without water)49,0892
Polymers49,0892
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-24 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.906, 78.906, 315.147
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody Fab fragment of human anti-HIV antibody N12-i2, heavy chain


Mass: 25650.572 Da / Num. of mol.: 1 / Fragment: Fab heavy chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody Fab fragment of human anti-HIV antibody N12-i2, light chain


Mass: 23437.988 Da / Num. of mol.: 1 / Fragment: Fab light chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.01 M Ni (II) chloride hexahydrate, 0.1 M Tris HCl, pH 8.5, 20% Polyethylene glycol monomethyl ether 2,000, , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979464 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979464 Å / Relative weight: 1
ReflectionResolution: 1.95→68.335 Å / Num. all: 43646 / Num. obs: 43613 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 20.2 % / Rmerge(I) obs: 0.094 / Rsym value: 0.065 / Net I/σ(I): 40
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4255 / Rsym value: 0.618 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RZ8

1rz8


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.988 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23612 2189 5 %RANDOM
Rwork0.20316 ---
all0.20483 2946 --
obs0.20483 41215 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.489 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20.87 Å20 Å2
2--1.74 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 0 298 3559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223340
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.9544541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92924.091132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23915536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.331516
X-RAY DIFFRACTIONr_chiral_restr0.1430.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212511
X-RAY DIFFRACTIONr_mcbond_it1.0531.52136
X-RAY DIFFRACTIONr_mcangle_it1.84923458
X-RAY DIFFRACTIONr_scbond_it3.0131204
X-RAY DIFFRACTIONr_scangle_it4.6584.51082
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 148 -
Rwork0.284 2946 -
obs--99.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1233-0.41290.49220.60250.44275.47220.0658-0.2357-0.0695-0.1153-0.03870.0998-0.0282-0.5734-0.0270.03310.0359-0.00130.2040.02470.136714.785126.79947.8044
21.7442-0.2037-0.63620.15130.29483.79290.0301-0.40280.0049-0.02430.0714-0.01310.12750.6088-0.10150.02330.03190.00780.1920.01210.11431.105827.950314.2171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H-10 - 9999
2X-RAY DIFFRACTION2L-10 - 9999

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