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- PDB-4fze: Crystal structure of N26_i1 Fab, an ADCC mediating anti-HIV-1 ant... -

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Basic information

Entry
Database: PDB / ID: 4fze
TitleCrystal structure of N26_i1 Fab, an ADCC mediating anti-HIV-1 antibody.
Components
  • N26_i1 Fab heavy chain
  • N26_i1 Fab light chain
KeywordsIMMUNE SYSTEM / ADCC / ANTI-HIV-1 ENV ANTIBODY N26_i1 / VIRAL GLYCOPROTEIN GP120 / HIV-1 ENV / CD4I ANTIBODY / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsTolbert, W.D. / Wu, X. / Pazgier, M.
CitationJournal: To be Published
Title: Crystal structure of N26_i1 Fab, an ADCC mediating anti-HIV-1 antibody.
Authors: Tolbert, W.D. / Wu, X. / Pazgier, M.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3May 19, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: N26_i1 Fab light chain
H: N26_i1 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0682
Polymers47,0682
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-25 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.636, 124.452, 41.433
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-362-

HOH

21L-400-

HOH

31H-397-

HOH

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Components

#1: Antibody N26_i1 Fab light chain


Mass: 22514.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody N26_i1 Fab heavy chain


Mass: 24553.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo Sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5, and 30% PEG 8000, 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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2012 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. all: 32431 / Num. obs: 32042 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 1.1 / Num. unique all: 2748 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
PHASERphasing
CNS(phenix.refine: 1.8_1069)refinement
REFMAC(phenix.refine: 1.8_1069)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D9L

4d9l


Resolution: 1.999→41.088 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 3202 10 %RANDOM
Rwork0.1856 ---
all0.1913 32446 --
obs0.1913 32031 98.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→41.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 0 252 3461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073290
X-RAY DIFFRACTIONf_angle_d1.1454489
X-RAY DIFFRACTIONf_dihedral_angle_d14.2191158
X-RAY DIFFRACTIONf_chiral_restr0.071519
X-RAY DIFFRACTIONf_plane_restr0.005571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.0290.35241240.33481064X-RAY DIFFRACTION84
2.029-2.06080.35671350.30261138X-RAY DIFFRACTION91
2.0608-2.09450.34141260.29241235X-RAY DIFFRACTION97
2.0945-2.13070.3271310.28131261X-RAY DIFFRACTION100
2.1307-2.16940.28111450.27231279X-RAY DIFFRACTION100
2.1694-2.21110.35221280.25911272X-RAY DIFFRACTION100
2.2111-2.25620.32951520.24591252X-RAY DIFFRACTION100
2.2562-2.30530.30381510.25181277X-RAY DIFFRACTION100
2.3053-2.35890.28651280.22951242X-RAY DIFFRACTION100
2.3589-2.41790.26811570.21681261X-RAY DIFFRACTION100
2.4179-2.48330.26811820.2171226X-RAY DIFFRACTION100
2.4833-2.55630.31071380.21771255X-RAY DIFFRACTION100
2.5563-2.63880.29611530.20151256X-RAY DIFFRACTION100
2.6388-2.73310.26371400.19711283X-RAY DIFFRACTION100
2.7331-2.84250.26191530.18751254X-RAY DIFFRACTION100
2.8425-2.97190.26951470.19081267X-RAY DIFFRACTION100
2.9719-3.12850.26651520.18341260X-RAY DIFFRACTION100
3.1285-3.32440.24771180.17541280X-RAY DIFFRACTION100
3.3244-3.5810.19721470.16631270X-RAY DIFFRACTION100
3.581-3.94110.20691020.15841314X-RAY DIFFRACTION100
3.9411-4.51080.18151330.13721283X-RAY DIFFRACTION100
4.5108-5.68070.19141330.13511292X-RAY DIFFRACTION100
5.6807-41.09680.20161270.16631308X-RAY DIFFRACTION100
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)
11.5762-0.13160.04471.785-1.20691.39790.04870.0773-0.0325-0.0059-0.0620.00390.02540.06680.03550.13820.00250.01380.1469-0.06490.1676-14.922113.121710.0222
22.3026-0.85540.49731.3185-0.99741.6003-0.0077-0.07780.09120.0690.08740.1146-0.0566-0.122-0.05890.15420.00560.01670.1509-0.07450.1456-32.245117.974112.6859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 210 )
2X-RAY DIFFRACTION2chain 'H' and (resid 1 through 215 )

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