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- PDB-7z3w: Crystal structure of the AAL160 Fab -

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Basic information

Entry
Database: PDB / ID: 7z3w
TitleCrystal structure of the AAL160 Fab
Components
  • AAL160 Fab heavy-chain
  • AAL160 Fab light-chain
KeywordsIMMUNE SYSTEM / monoclonal antibody
Function / homologyChem-ETE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsRondeau, J.M. / Lehmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2023
Title: "Redirecting an anti-IL-1 beta antibody to bind a new, unrelated and computationally predicted epitope on hIL-17A".
Authors: Fischman, S. / Levin, I. / Rondeau, J.M. / Strajbl, M. / Lehmann, S. / Huber, T. / Nimrod, G. / Cebe, R. / Omer, D. / Kovarik, J. / Bernstein, S. / Sasson, Y. / Demishtein, A. / Shlamkovich, ...Authors: Fischman, S. / Levin, I. / Rondeau, J.M. / Strajbl, M. / Lehmann, S. / Huber, T. / Nimrod, G. / Cebe, R. / Omer, D. / Kovarik, J. / Bernstein, S. / Sasson, Y. / Demishtein, A. / Shlamkovich, T. / Bluvshtein, O. / Grossman, N. / Barak-Fuchs, R. / Zhenin, M. / Fastman, Y. / Twito, S. / Vana, T. / Zur, N. / Ofran, Y.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: AAL160 Fab heavy-chain
L: AAL160 Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1869
Polymers47,7282
Non-polymers1,4587
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-28 kcal/mol
Surface area19760 Å2
Unit cell
Length a, b, c (Å)62.173, 89.832, 123.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody AAL160 Fab heavy-chain


Mass: 24228.166 Da / Num. of mol.: 1 / Fragment: Fab heavy-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): hybridoma / Production host: Homo sapiens (human)
#2: Antibody AAL160 Fab light-chain


Mass: 23500.119 Da / Num. of mol.: 1 / Fragment: Fab light-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Hybridoma / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H20O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 3.62 Å3/Da / Density % sol: 66.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1M CHES pH 9.5, 50% (w/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.7998 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 18, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7998 Å / Relative weight: 1
ReflectionResolution: 2→28 Å / Num. obs: 47440 / % possible obs: 99.9 % / Redundancy: 8.34 % / Biso Wilson estimate: 35.22 Å2 / Rmerge(I) obs: 0.05 / Χ2: 0.891 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.070.38146700.671100
2.07-2.150.26846500.6991100
2.15-2.250.20546670.727199.9
2.25-2.370.17247120.769199.9
2.37-2.520.14746590.794199.9
2.52-2.710.11247310.8761100
2.71-2.990.07647210.9831100
2.99-3.420.04947531.112199.9
3.42-4.30.03547921.072199.6
4.3-280.03350030.876199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-20001.96.1data reduction
SCALEPACK1.96.1data scaling
AMoRE3.4phasing
BUSTER2.11.8refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIM.PDB

1mim


Resolution: 2→16.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 4778 10.07 %RANDOM
Rwork0.1957 ---
obs0.1979 47440 99.9 %-
Displacement parametersBiso max: 88.28 Å2 / Biso mean: 37.5 Å2 / Biso min: 23.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.6312 Å20 Å20 Å2
2---4.7977 Å20 Å2
3---4.1665 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2→16.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 98 317 3686
Biso mean--61.29 47.18 -
Num. residues----428
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1180SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes556HARMONIC5
X-RAY DIFFRACTIONt_it3447HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion444SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2894SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3447HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4653HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion4.17
X-RAY DIFFRACTIONt_other_torsion14.72
LS refinement shellResolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2333 99 10.43 %
Rwork0.2195 850 -
all0.221 949 -
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)
10.6706-0.4031-0.32160.75960.48110.682-0.0527-0.0230.0977-0.04330.0735-0.02290.1093-0.0502-0.0208-0.0341-0.0311-0.0054-0.03110.0213-0.014211.423351.941656.2875
20.5051-0.2843-0.36510.20240.25531.6935-0.0557-0.0907-0.01340.06870.0315-0.02710.16940.09830.02430.0042-0.0176-0.0076-0.05410.0157-0.041716.098437.00564.7283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|* }H1 - 218
2X-RAY DIFFRACTION2{ L|* }L1 - 214

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