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- PDB-5nbi: Principles for computational design of antibodies -

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Basic information

Entry
Database: PDB / ID: 5nbi
TitlePrinciples for computational design of antibodies
Components(Design of antibodies) x 2
KeywordsIMMUNE SYSTEM / antibodies
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDym, O. / Fleishman, S.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Principles for computational design of binding antibodies.
Authors: Baran, D. / Pszolla, M.G. / Lapidoth, G.D. / Norn, C. / Dym, O. / Unger, T. / Albeck, S. / Tyka, M.D. / Fleishman, S.J.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 12, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.5Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Design of antibodies
L: Design of antibodies


Theoretical massNumber of molelcules
Total (without water)48,8942
Polymers48,8942
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-22 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.909, 67.909, 182.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody Design of antibodies


Mass: 25035.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody Design of antibodies


Mass: 23858.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M NH4CH3CO2 0.05M Mg(CH3CO2)2 0.05M Cacodylate pH=6.5 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.1→60.73 Å / Num. obs: 28196 / % possible obs: 93 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 10429 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ9, 4JFZ

3qq9

4jfz


Resolution: 2.1→60.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 14.506 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.193 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 1405 4.9 %RANDOM
Rwork0.21794 ---
obs0.2199 27279 97.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 54.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 2.1→60.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 0 8 3311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193392
X-RAY DIFFRACTIONr_bond_other_d0.0020.022977
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9384616
X-RAY DIFFRACTIONr_angle_other_deg0.90936962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2395431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13224.307137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99715524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3151513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
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_it2.6033.0541733
X-RAY DIFFRACTIONr_mcbond_other2.63.0531732
X-RAY DIFFRACTIONr_mcangle_it3.8424.5682161
X-RAY DIFFRACTIONr_mcangle_other3.8414.5682162
X-RAY DIFFRACTIONr_scbond_it2.973.3731658
X-RAY DIFFRACTIONr_scbond_other2.9693.3741659
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5714.9142456
X-RAY DIFFRACTIONr_long_range_B_refined6.40534.8613440
X-RAY DIFFRACTIONr_long_range_B_other6.40434.8693441
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 84 -
Rwork0.286 1959 -
obs--97.52 %
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)
12.8632-0.31070.18030.9379-0.69012.9828-0.0755-0.2353-0.0079-0.05450.05480.0138-0.0122-0.25380.02080.0247-0.0030.03690.06690.00890.156362.10921.63202.937
22.9306-0.88530.32540.286-0.10941.6589-0.1246-0.0705-0.0159-0.00530.05330.0156-0.17070.04460.07130.1441-0.07280.02020.05040.02370.212173.44828.713190.504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H3 - 221
2X-RAY DIFFRACTION2L1 - 216

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