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- PDB-9axs: Crystal Structure of HY18-5B1_Ch Fab in the Apo Conformation -

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Basic information

Entry
Database: PDB / ID: 9axs
TitleCrystal Structure of HY18-5B1_Ch Fab in the Apo Conformation
Components
  • HY18-5B1_Ch Fab Heavy Chain
  • HY18-5B1_Ch Fab Light Chain
KeywordsIMMUNE SYSTEM / opioids / mAb / apo / cross-reactive
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsMcGovern, M.R. / Rodarte, J.V. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)UG3 DA047711 United States
CitationJournal: Acs Omega / Year: 2024
Title: Structure-Based Engineering of Monoclonal Antibodies for Improved Binding to Counteract the Effects of Fentanyl and Carfentanil.
Authors: Rodarte, J. / Baehr, C. / Hicks, D. / McGovern, M. / Zhang, Y. / Silva-Ortiz, P. / Hannon, B. / Duddu, S. / Pancera, M. / Pravetoni, M.
History
DepositionMar 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: HY18-5B1_Ch Fab Heavy Chain
L: HY18-5B1_Ch Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7054
Polymers48,5212
Non-polymers1842
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-29 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.328, 61.321, 76.576
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-474-

HOH

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Components

#1: Antibody HY18-5B1_Ch Fab Heavy Chain


Mass: 24925.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody HY18-5B1_Ch Fab Light Chain


Mass: 23595.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 27% PEG 8000, 0.02M cobalt chloride, 0.15M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 26804 / % possible obs: 98.8 % / Redundancy: 3.2 % / CC1/2: 0.974 / CC star: 0.993 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.063 / Rrim(I) all: 0.116 / Χ2: 3.225 / Net I/σ(I): 11.1 / Num. measured all: 85519
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.04-2.083.10.35713370.710.9110.2360.4291.19699
2.08-2.113.20.29113410.8810.9680.1910.3490.83999.6
2.11-2.153.20.2813350.8950.9720.1830.3361.02299.4
2.15-2.23.20.2313260.9260.980.1510.2771.02199.7
2.2-2.253.20.23713660.8990.9730.1580.2861.25698.6
2.25-2.33.20.2212980.9180.9780.1440.2641.29498.3
2.3-2.3530.18513100.940.9840.1250.2241.38896
2.35-2.423.10.17313170.9480.9870.1170.211.38497.7
2.42-2.493.30.16513280.9560.9890.1060.1971.71799.7
2.49-2.573.30.14813520.9670.9910.0950.1761.70199.4
2.57-2.663.20.13713490.9630.990.0890.1642.15799.3
2.66-2.773.20.12213090.9710.9930.080.1472.62598.3
2.77-2.893.10.1113280.970.9920.0740.1332.74297.4
2.89-3.053.30.1113560.9720.9930.0710.1313.66899.2
3.05-3.243.30.09513350.9820.9960.0610.1134.31199.6
3.24-3.493.30.09113570.9790.9950.0590.1085.40299.3
3.49-3.8430.08813350.9730.9930.0590.1066.51297.6
3.84-4.393.30.08413580.9820.9950.0540.17.236100
4.39-5.543.20.07913670.9830.9960.0510.0947.2298.6
5.54-503.20.08514000.9730.9930.0560.1028.95799.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→45.79 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1294 4.83 %
Rwork0.2004 --
obs0.2023 26780 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 12 179 3433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023326
X-RAY DIFFRACTIONf_angle_d0.5164536
X-RAY DIFFRACTIONf_dihedral_angle_d6.107468
X-RAY DIFFRACTIONf_chiral_restr0.043519
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.120.26121320.22842752X-RAY DIFFRACTION97
2.12-2.220.25851350.20672834X-RAY DIFFRACTION99
2.22-2.330.29061220.21812851X-RAY DIFFRACTION98
2.33-2.480.2591320.22082781X-RAY DIFFRACTION98
2.48-2.670.26571450.23262884X-RAY DIFFRACTION99
2.67-2.940.26111440.22632793X-RAY DIFFRACTION98
2.94-3.370.24541660.21242833X-RAY DIFFRACTION99
3.37-4.240.21981530.18442853X-RAY DIFFRACTION99
4.24-45.790.20891650.17732905X-RAY DIFFRACTION99

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