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- PDB-4g5z: Crystal structure of the therapeutical antibody fragment of canak... -

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Basic information

Entry
Database: PDB / ID: 4g5z
TitleCrystal structure of the therapeutical antibody fragment of canakinumab in its unbound state
Components
  • canakinumab antibody fragment heavy chain
  • canakinumab antibody fragment light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / antibody / immunoglobulin / interleukine-1beta binding / cytokine / blood system
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological specieshomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBlech, M. / Hoerer, S.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: One target-two different binding modes: Structural insights into gevokizumab and canakinumab interactions to interleukin-1beta
Authors: Blech, M. / Peter, D. / Fischer, P. / Bauer, M.M. / Hafner, M. / Zeeb, M. / Nar, H.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Other
Revision 1.3Sep 13, 2023Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: canakinumab antibody fragment heavy chain
L: canakinumab antibody fragment light chain


Theoretical massNumber of molelcules
Total (without water)46,4992
Polymers46,4992
Non-polymers00
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-29 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.216, 54.585, 94.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody canakinumab antibody fragment heavy chain


Mass: 23349.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) homo sapiens (human)
#2: Antibody canakinumab antibody fragment light chain


Mass: 23149.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: crystal grown in 11% w/v PEG 3350 and 0.14M Tris-HCL equilibrated against a reservoir solution of 24% w/v PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→94.1 Å / Num. all: 250861 / Num. obs: 37442 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.113
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSdata scaling
autoPROCdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
autoPROCdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ5 and 3BKJ

1pz5

3bkj


Resolution: 1.83→40 Å / Cor.coef. Fo:Fc: 0.9336 / Cor.coef. Fo:Fc free: 0.9133 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1869 5 %RANDOM
Rwork0.1933 ---
obs0.1948 37375 99.36 %-
all-37442 --
Displacement parametersBiso mean: 19.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.391 Å20 Å20 Å2
2--1.628 Å20 Å2
3----0.237 Å2
Refine analyzeLuzzati coordinate error obs: 0.227 Å
Refinement stepCycle: LAST / Resolution: 1.83→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 0 0 445 3718
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073355HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014569HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1105SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes491HARMONIC5
X-RAY DIFFRACTIONt_it3355HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion15.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
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_contact4064SEMIHARMONIC4
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2898 121 4.47 %
Rwork0.2479 2587 -
all0.2498 2708 -
obs--99.36 %
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)
10.46670.5549-0.53010.7778-0.52640.6559-0.00140.1442-0.01310.02450.08940.02010.0504-0.095-0.088-0.05640.0035-0.016-0.01480.0051-0.017-4.9054-6.04411.9121
20.38250.1565-0.02760.6297-0.55161.03070.01980.0448-0.03430.06570.0059-0.0394-0.06690.0487-0.0257-0.051800.012-0.042-0.0326-0.036811.2919-0.67226.952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|1 - H|218 }H1 - 218
2X-RAY DIFFRACTION2{ L|1 - L|212 }L1 - 212

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