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- PDB-8t9y: Structure of VHH-Fab complex with engineered Elbow FNQIKG and Cry... -

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Basic information

Entry
Database: PDB / ID: 8t9y
TitleStructure of VHH-Fab complex with engineered Elbow FNQIKG and Crystal Kappa regions
Components
  • Fab heavy chain
  • Fab light chain
  • VHH domain
KeywordsIMMUNE SYSTEM / NabFab / Nanobody / Antibody Fragment
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsFilippova, E.V. / Thompson, I. / Kossiakoff, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Protein Sci. / Year: 2024
Title: Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes.
Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / ...Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / Atwell, S. / Kossiakoff, A.A. / Sidhu, S.S.
History
DepositionJun 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VHH domain
L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1625
Polymers62,9503
Non-polymers2122
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-24 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.565, 73.565, 207.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody VHH domain


Mass: 14170.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET26B+ / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Antibody Fab light chain


Mass: 23025.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: RH2.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
#3: Antibody Fab heavy chain


Mass: 25753.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: RH2.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1 M Citric acid, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.52→103.62 Å / Num. obs: 20161 / % possible obs: 100 % / Redundancy: 25.9 % / CC1/2: 0.99 / Rpim(I) all: 0.03 / Net I/σ(I): 19.2
Reflection shellResolution: 2.52→2.62 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2220 / CC1/2: 0.69 / Rpim(I) all: 0.51 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 32.877 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 0.727 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28482 1006 5 %RANDOM
Rwork0.21447 ---
obs0.21802 19074 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.513 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å2-0 Å20 Å2
2--3.66 Å20 Å2
3----7.33 Å2
Refinement stepCycle: 1 / Resolution: 2.52→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 14 37 4172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124233
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.6345745
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5215529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01922.513187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35715663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2931518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023200
X-RAY DIFFRACTIONr_gen_planes_other
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_mcbond_it2.0715.3882143
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5868.0562663
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0515.532089
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.92270.9015979
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 72 -
Rwork0.411 1347 -
obs--98.68 %
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)
10.25180.3699-0.16251.3332-1.67274.6477-0.12890.3191-0.0475-0.29270.3456-0.0717-0.1139-0.4692-0.21670.2613-0.030.00840.5612-0.04320.1588-13.6437.626-40.197
22.5436-3.3164-4.15384.3265.41776.79620.35480.05410.1035-0.4784-0.0991-0.1385-0.569-0.1558-0.25570.21240.1123-0.1470.55160.36810.6219-26.10916.116-42.371
314.4145.3845-0.3322.3057-0.74081.32950.05020.31010.6949-0.02420.04690.290.12230.0369-0.09710.2523-0.00080.00740.3057-0.03620.2936-14.9014.765-32.029
40.4511-0.3621.07782.86662.13456.56410.15240.1340.12550.6617-0.0678-0.29420.86130.6114-0.08460.5077-0.08460.10050.2951-0.04720.20121.51311.416-3.387
54.77021.4920.91021.84771.88762.03980.0043-0.00350.10560.0537-0.01360.04870.0872-0.01260.00930.28670.03490.07460.21340.0320.3346-6.58711.781-13.443
62.70531.15131.85580.99061.94073.92980.2991-0.5143-0.21470.1451-0.172-0.08430.2767-0.1684-0.1270.27710.06070.06250.21260.03920.3968-5.899.388-8.353
71.0235-0.7632-0.21630.9956-0.84482.4936-0.0189-0.0929-0.16630.0045-0.0710.0676-0.01430.28030.08990.0457-0.07780.05370.4773-0.09010.3527-5.61112.66323.791
82.2020.0355-1.96970.7146-0.08341.798-0.0712-0.1939-0.00090.00540.20180.03370.03930.1647-0.13050.0514-0.01280.04060.483-0.04210.399-4.69612.55627.722
94.23592.2967-2.23033.29631.63115.12880.3577-0.18610.58370.5959-0.8560.87010.4533-0.93740.49830.2349-0.05770.190.4239-0.25670.4769-27.6859.133-11.342
101.55-0.4121-3.9715.0161-0.855910.9587-0.13190.1358-0.10580.2205-0.02190.72520.4886-0.4450.15380.1783-0.25170.18210.3887-0.18630.5203-31.6862.796-8.216
111.86451.8803-0.17112.06010.66614.65590.2829-0.08820.29330.2894-0.25260.280.2619-0.7016-0.03020.22880.04910.08350.3437-0.09170.4347-20.9227.307-12.744
123.15780.5155-0.95440.85580.85331.6196-0.01440.1578-0.4428-0.0282-0.1263-0.0815-0.0551-0.19770.14060.0637-0.07650.00810.4481-0.15830.4166-16.92319.16221.099
136.21674.50073.42234.06243.78024.0422-0.07780.16990.166-0.2151-0.13220.1614-0.3618-0.24110.20990.1387-0.058-0.02390.4059-0.11850.3088-21.2226.50324.506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 104
2X-RAY DIFFRACTION2A111 - 125
3X-RAY DIFFRACTION3A126 - 137
4X-RAY DIFFRACTION4L5 - 18
5X-RAY DIFFRACTION5L19 - 83
6X-RAY DIFFRACTION6L84 - 124
7X-RAY DIFFRACTION7L125 - 183
8X-RAY DIFFRACTION8L184 - 231
9X-RAY DIFFRACTION9H1 - 62
10X-RAY DIFFRACTION10H63 - 98
11X-RAY DIFFRACTION11H99 - 138
12X-RAY DIFFRACTION12H139 - 209
13X-RAY DIFFRACTION13H210 - 238

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