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- PDB-4kq4: Crystal structure of Anti-IL-17A antibody CNTO7357 -

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Basic information

Entry
Database: PDB / ID: 4kq4
TitleCrystal structure of Anti-IL-17A antibody CNTO7357
Components
  • CNTO7357 heavy chain
  • CNTO7357 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / NICKEL (II) ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2014
Title: Antibody modeling assessment II. Structures and models.
Authors: Teplyakov, A. / Luo, J. / Obmolova, G. / Malia, T.J. / Sweet, R. / Stanfield, R.L. / Kodangattil, S. / Almagro, J.C. / Gilliland, G.L.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: CNTO7357 light chain
H: CNTO7357 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0333
Polymers47,9752
Non-polymers591
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-34 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.500, 65.500, 99.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody CNTO7357 light chain


Mass: 23551.162 Da / Num. of mol.: 1
Fragment: Fab (mouse variable domain, human constant domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK293E / Production host: Homo sapiens (human)
#2: Antibody CNTO7357 heavy chain


Mass: 24423.385 Da / Num. of mol.: 1
Fragment: Fab (mouse variable domain, human constant domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK293E / Production host: Homo sapiens (human)
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 18% PEG8000, cryoprotectant: 0.1 M HEPES, pH 7.5, 20% PEG8000, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 13, 2008 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 17241 / Num. obs: 17241 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.3
Reflection shellResolution: 2.45→2.52 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 4.3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZTX

1ztx


Resolution: 2.45→15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.897 / SU B: 30.859 / SU ML: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.592 / ESU R Free: 0.319 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27903 865 5 %RANDOM
Rwork0.20957 ---
all0.21281 16321 --
obs0.21281 16321 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.5 Å20 Å2
2--1.01 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 1 63 3412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213431
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9384666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1495437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0724.03134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.115555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6231513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212564
X-RAY DIFFRACTIONr_mcbond_it2.14822182
X-RAY DIFFRACTIONr_mcangle_it4.21243533
X-RAY DIFFRACTIONr_scbond_it28.717881249
X-RAY DIFFRACTIONr_scangle_it29.775881133
LS refinement shellResolution: 2.45→2.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 66 -
Rwork0.258 1210 -
obs--97.9 %
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)
11.9616-0.9391-0.7742.3670.75324.0541-0.00980.468-0.21310.24490.12330.4349-0.1972-0.6415-0.11350.28360.240.08030.61770.08020.2266-21.4967.652-4.0234
25.3507-0.1562-0.4120.7146-0.53562.93340.31830.5630.43290.7370.0226-0.1224-0.50260.0941-0.34090.85020.1461-0.0810.17190.01980.12959.498815.46149.5569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION1H1 - 117
3X-RAY DIFFRACTION2L108 - 214
4X-RAY DIFFRACTION2H118 - 225

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