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- PDB-4g6k: Crystal structure of the therapeutic antibody binding fragment of... -

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Basic information

Entry
Database: PDB / ID: 4g6k
TitleCrystal structure of the therapeutic antibody binding fragment of gevokizumab in its unbound state
Components
  • heavy chain of gevokizumab antibody binding fragment
  • light chain of gevokizumab antibody binding fragment
KeywordsIMMUNE SYSTEM / immunoglobulin fold / cytokine / interleukine-1beta
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological specieshomo Sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: heavy chain of gevokizumab antibody binding fragment
L: light chain of gevokizumab antibody binding fragment


Theoretical massNumber of molelcules
Total (without water)46,7912
Polymers46,7912
Non-polymers00
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-30 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.345, 75.092, 88.862
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 heavy chain of gevokizumab antibody binding fragment


Mass: 23420.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo Sapiens, Mus musculus / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody light chain of gevokizumab antibody binding fragment


Mass: 23371.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo Sapiens, Mus musculus / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 14.3% w/v PEG 3350 and 0.14M tri-sodium citrate at pH 5.0 equilibrated against 24% w/v PEG 3350, 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: Nov 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.9→57.4 Å / Num. all: 284279 / Num. obs: 41364 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 24.43 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.084 / Net I/σ(I): 19.4
Reflection shellHighest resolution: 1.9 Å

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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: 1.9→27.75 Å / Cor.coef. Fo:Fc: 0.9458 / Cor.coef. Fo:Fc free: 0.9335 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 2007 5.03 %RANDOM
Rwork0.1826 ---
obs0.184 39868 99.98 %-
all-41364 --
Displacement parametersBiso mean: 28.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.2188 Å20 Å20 Å2
2--1.0203 Å20 Å2
3----2.2391 Å2
Refine analyzeLuzzati coordinate error obs: 0.212 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 0 510 3801
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073373HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034593HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1117SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes488HARMONIC5
X-RAY DIFFRACTIONt_it3373HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion15.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion451SEMIHARMONIC5
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_contact4052SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2164 139 4.79 %
Rwork0.1991 2761 -
all0.1999 2900 -
obs--99.98 %
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)
10.82310.0107-0.73580.4988-0.16060.99880.014-0.08660.01460.01780.00740.0331-0.0080.1013-0.0214-0.0499-0.0095-0.01-0.0407-0.0052-0.005945.629317.237-27.8362
21.0443-0.1417-0.44510.83690.11360.57820.0234-0.11010.20680.12520.0191-0.0396-0.06070.0632-0.0425-0.0538-0.0113-0.0067-0.0839-0.0376-0.034735.826632.1798-26.6382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|1 - H|220 }H1 - 220
2X-RAY DIFFRACTION2{ L|1 - L|212 }L1 - 212

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