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- PDB-7n07: Crystal structure of the apo 3D6 antibody fragment -

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Basic information

Entry
Database: PDB / ID: 7n07
TitleCrystal structure of the apo 3D6 antibody fragment
Components
  • Fab 3D6 heavy chain
  • Fab 3D6 light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / anti-HIV / gp41
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCook, J.D. / Lee, J.E.
Funding support Canada, 5items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-115066 Canada
Canadian Institutes of Health Research (CIHR)PJT-173301 Canada
Ontario Early Researcher AwardsER-13-09-116 Canada
Canada Research Chairs950-231672 Canada
Canada Foundation for Innovation Canada
CitationJournal: Commun Biol / Year: 2022
Title: Conformational plasticity of the HIV-1 gp41 immunodominant region is recognized by multiple non-neutralizing antibodies.
Authors: Cook, J.D. / Khondker, A. / Lee, J.E.
History
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab 3D6 heavy chain
L: Fab 3D6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1134
Polymers49,9212
Non-polymers1922
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-49 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.429, 84.429, 161.022
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Fab 3D6 heavy chain


Mass: 26649.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody Fab 3D6 light chain


Mass: 23270.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.17 M ammonium sulfate, 25.5% (w/v) PEG 4000, and 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9801 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 27, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.4→48 Å / Num. obs: 23589 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.029 / Rrim(I) all: 0.132 / Net I/σ(I): 20.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.491.5724300.8770.3411.608100
8.98-47.950.0395480.9990.0090.0499.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.5.28data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFB

1dfb


Resolution: 2.4→48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.664 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 2000 8.5 %RANDOM
Rwork0.1948 ---
obs0.1986 21524 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 134.35 Å2 / Biso mean: 61.482 Å2 / Biso min: 27.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 2.4→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 10 79 3382
Biso mean--92.98 45.79 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0173381
X-RAY DIFFRACTIONr_bond_other_d0.0010.0193079
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.8554598
X-RAY DIFFRACTIONr_angle_other_deg0.9722.7027127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26922.808146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51415539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2011514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02768
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 143 -
Rwork0.294 1541 -
all-1684 -
obs--100 %
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)
13.75113.38261.18898.6152.27263.2424-0.36710.82080.2007-0.88230.36520.2161-0.2565-0.00810.00190.1086-0.075-0.05280.31930.06710.10363.32775.3694.785
26.23671.3354-0.19575.1849-0.74822.19290.0312-0.07830.35660.25380.04430.00410.0189-0.0313-0.07540.01870.0091-0.01370.14350.04190.07472.12173.25814.675
312.2918-2.774-3.75553.37351.61221.4804-0.12010.15070.9773-0.76970.3967-0.3588-0.13220.232-0.27650.3633-0.15370.00980.36630.10010.246331.33791.999-0.77
47.9118-2.3235-1.27484.65610.64460.2857-0.10340.23240.2988-0.99810.2244-0.0769-0.09820.0948-0.1210.3948-0.1840.00670.42160.06030.256128.42886.708-3.589
59.3892-1.8099-0.7133.33180.17854.83660.0791-0.2252-0.02130.214-0.03330.3157-0.1025-0.1298-0.04580.03150.0138-00.19740.02950.126825.15963.65123.835
65.35671.5367-3.64764.7589-5.84313.5979-0.024-0.2995-0.0443-0.3810.30070.74070.6639-0.4379-0.27670.0438-0.0386-0.02920.22480.00070.315714.17259.66321.536
76.1716-1.55533.34764.7089-1.37026.01450.14810.6048-0.2477-0.6399-0.03270.28720.6240.3557-0.11540.1760.0036-0.04420.2565-0.02430.278719.88658.8212.671
88.02621.9446-2.0754.814-6.434111.12580.13420.53-0.0753-0.0785-0.04610.10890.09940.2625-0.08810.01560.0122-0.00170.1977-0.01680.172928.53960.0516.102
911.1461-4.4973-0.05092.2023-0.75217.2835-0.15780.0285-0.40660.04830.27720.37020.3351-0.8205-0.11950.0514-0.0602-0.0350.31480.13650.263614.60765.68119.736
107.90466.5632-5.36525.5581-4.44433.64420.1492-0.0090.6270.09260.25520.3494-0.09620.0546-0.40440.0533-0.1058-0.01540.9271-0.07890.578238.87970.76914.381
115.2341-2.76530.361812.4779-1.46431.9747-0.1562-0.60731.1014-0.34430.4952-0.9402-0.42090.3079-0.3390.1702-0.15570.12430.5065-0.15950.468439.6591.7136.281
125.9254-3.3282-1.20349.756-2.86921.8598-0.2877-0.83670.5194-0.12450.62270.05210.13830.0904-0.33490.1766-0.055-0.00870.7602-0.00130.252937.47485.42810.779
132.9737-2.2775-0.154413.0312-1.5293.0443-0.3686-0.37291.18730.20420.399-1.77-0.50350.4031-0.03050.258-0.16740.00340.6271-0.27830.832743.94895.6328.398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 33
2X-RAY DIFFRACTION2H34 - 75
3X-RAY DIFFRACTION3H112 - 145
4X-RAY DIFFRACTION4H146 - 213
5X-RAY DIFFRACTION5L1 - 25
6X-RAY DIFFRACTION6L26 - 38
7X-RAY DIFFRACTION7L39 - 69
8X-RAY DIFFRACTION8L70 - 83
9X-RAY DIFFRACTION9L84 - 99
10X-RAY DIFFRACTION10L100 - 111
11X-RAY DIFFRACTION11L112 - 148
12X-RAY DIFFRACTION12L149 - 172
13X-RAY DIFFRACTION13L173 - 209

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