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- PDB-8tfr: Apo Fab from C10-S66K antibody -

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Basic information

Entry
Database: PDB / ID: 8tfr
TitleApo Fab from C10-S66K antibody
Components
  • Heavy chain from Fab of C10_S66K antibody
  • Immunoglobulin G-binding protein G
  • Light chain from Fab of C10_S66K antibody
KeywordsIMMUNE SYSTEM / Antibody / fentanyl analogue / carfentanil / opioid
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsPholcharee, T. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)U01DA046232 United States
Citation
Journal: Acs Chem Neurosci / Year: 2023
Title: An Engineered Human-Antibody Fragment with Fentanyl Pan-Specificity That Reverses Carfentanil-Induced Respiratory Depression.
Authors: Eubanks, L.M. / Pholcharee, T. / Oyen, D. / Natori, Y. / Zhou, B. / Wilson, I.A. / Janda, K.D.
#1: Journal: Biorxiv / Year: 2023
Title: An Engineered Human-Antibody Fragment with Fentanyl Pan-Specificity that Reverses Carfentanil-Induced Respiratory Depression.
Authors: Eubanks, L.M. / Pholcharee, T. / Oyen, D. / Natori, Y. / Zhou, B. / Wilson, I.A. / Janda, K.D.
History
DepositionJul 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Immunoglobulin G-binding protein G
A: Heavy chain from Fab of C10_S66K antibody
B: Light chain from Fab of C10_S66K antibody


Theoretical massNumber of molelcules
Total (without water)53,9873
Polymers53,9873
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.913, 92.913, 123.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 7348.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P19909
#2: Antibody Heavy chain from Fab of C10_S66K antibody


Mass: 23740.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Light chain from Fab of C10_S66K antibody


Mass: 22898.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Na3-citrate, pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 12321 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.989 / Net I/σ(I): 13.1
Reflection shellResolution: 2.96→3.01 Å / Num. unique obs: 596 / CC1/2: 0.502

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→49.1 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 650 5.29 %
Rwork0.2114 --
obs0.2141 12296 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.99→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 0 3458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043542
X-RAY DIFFRACTIONf_angle_d0.7244868
X-RAY DIFFRACTIONf_dihedral_angle_d5.525495
X-RAY DIFFRACTIONf_chiral_restr0.047581
X-RAY DIFFRACTIONf_plane_restr0.007622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.220.34661440.31432255X-RAY DIFFRACTION98
3.22-3.540.34851160.27862334X-RAY DIFFRACTION100
3.54-4.050.29561370.24562335X-RAY DIFFRACTION100
4.05-5.10.26771330.18682339X-RAY DIFFRACTION100
5.11-49.10.20261200.17182383X-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)
13.13262.3891-1.78143.0673-0.29976.7195-0.18010.00971.3655-1.788-0.0664-0.65240.8390.96630.1470.89070.09210.17641.0988-0.10381.0546-19.8821-20.9608-34.5107
24.63482.65143.39968.9167-1.81934.4086-0.17631.07120.1694-1.3333-0.42810.33590.41661.25220.12441.0417-0.05580.13680.9022-0.12850.6189-26.4476-17.1313-37.9832
35.7017-6.4154-5.97487.26026.79526.3866-0.13541.25352.0934-2.336-1.1834-1.1897-2.47930.78380.67561.0425-0.08780.0730.99570.00021.4607-21.2116-7.9281-37.6394
42.7262-2.26523.06591.882-2.54253.50390.39921.37320.2636-1.2332-0.0724-1.53661.54582.2856-0.24191.15810.39350.42331.72150.02231.0387-16.2498-21.2587-42.0913
50.99121.2114-1.50464.8095-0.83923.6961-0.32180.0734-0.5561-0.12850.7646-0.27830.43750.0602-0.17020.72980.215-0.06520.8281-0.11890.3746-38.2195-29.329-6.3897
62.47281.1565-0.15625.5631-0.70223.6645-0.4922-0.0634-0.08490.90330.5572-0.25790.1165-0.7436-0.23370.69620.2223-0.14750.75-0.04530.3301-43.4087-31.60774.2499
73.07832.8669-1.7878.1833-1.05973.8164-0.60320.18180.6259-0.07041.00340.6523-0.743-1.0562-0.33320.89360.429-0.20910.7021-0.03730.4322-45.5058-19.3865-0.2429
81.92561.8601-1.20837.1856-2.78925.7225-0.07050.4850.195-0.41090.76830.85710.1652-0.7474-0.36750.70130.1989-0.06441.10190.06830.4276-53.1461-29.7812-0.7919
91.3361.1970.97316.5115-1.97692.2117-0.2727-0.0446-0.0220.89520.93570.2238-0.084-0.1076-0.33690.8020.2757-0.10830.8044-0.19470.3827-43.1578-26.3447-0.0429
100.66791.57171.62145.30751.67576.76-0.4145-0.2781.2129-0.09230.0073-0.6217-0.23880.66040.1920.35470.0052-0.13080.8778-0.32061.301-23.3157-7.6235-23.5869
114.76131.7982.77897.9233-0.17025.2103-0.23-0.17370.38330.3632-0.046-1.75250.49560.0365-0.37160.7067-0.0106-0.4110.8773-0.27510.8781-23.1173-14.2148-19.0779
121.80110.4060.79930.2650.07131.7694-0.5365-0.32680.89220.57-0.4423-1.5897-0.41831.70950.35880.88120.1141-0.36331.2179-0.21311.7767-11.5352-6.0097-12.8653
130.89480.6848-1.22041.29710.57594.5778-0.1392-0.38111.10970.4473-0.3179-0.91-1.14810.82610.07920.8311-0.2257-0.46840.8683-0.24671.5298-20.5488-3.9105-17.6967
140.75281.7484-0.85916.07770.10493.1358-0.3478-0.16131.20320.45650.2489-1.7406-0.41950.94540.35560.6277-0.2647-0.16810.9332-0.15571.3589-16.5034-11.0031-24.5899
150.64370.2672-1.08984.5052-1.05026.2829-0.0507-0.39840.01141.95820.7164-0.50160.04140.18780.2771.4830.8044-0.39410.9592-0.17020.3878-40.0559-9.49812.8359
163.53660.25630.79362.86610.21043.6294-0.7359-0.37870.96750.50430.5643-0.5953-0.9831-0.2990.29071.18820.142-0.51520.6878-0.38931.4468-31.56873.2355-15.5184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 5 through 27 )
2X-RAY DIFFRACTION2chain 'C' and (resid 28 through 41 )
3X-RAY DIFFRACTION3chain 'C' and (resid 42 through 46 )
4X-RAY DIFFRACTION4chain 'C' and (resid 47 through 60 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1 through 17 )
6X-RAY DIFFRACTION6chain 'A' and (resid 18 through 39 )
7X-RAY DIFFRACTION7chain 'A' and (resid 40 through 51 )
8X-RAY DIFFRACTION8chain 'A' and (resid 52 through 72 )
9X-RAY DIFFRACTION9chain 'A' and (resid 73 through 113 )
10X-RAY DIFFRACTION10chain 'A' and (resid 114 through 142 )
11X-RAY DIFFRACTION11chain 'A' and (resid 143 through 154 )
12X-RAY DIFFRACTION12chain 'A' and (resid 155 through 165 )
13X-RAY DIFFRACTION13chain 'A' and (resid 166 through 194 )
14X-RAY DIFFRACTION14chain 'A' and (resid 195 through 214 )
15X-RAY DIFFRACTION15chain 'B' and (resid 3 through 113 )
16X-RAY DIFFRACTION16chain 'B' and (resid 114 through 209 )

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