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- PDB-4trp: Crystal structure of monoclonal antibody against neuroblastoma as... -

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Basic information

Entry
Database: PDB / ID: 4trp
TitleCrystal structure of monoclonal antibody against neuroblastoma associated antigen.
Components
  • Heavy chain of monoclonal antibody against neuroblastoma associated antigen
  • Light chain of monoclonal antibody against neuroblastoma associated antigen
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsHorwacik, I. / Golik, P. / Grudnik, P. / Zdzalik, M. / Rokita, H. / Dubin, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
NCNN302 034 31/3063 Poland
CitationJournal: Mol.Cell Proteomics / Year: 2015
Title: Structural Basis of GD2 Ganglioside and Mimetic Peptide Recognition by 14G2a Antibody.
Authors: Horwacik, I. / Golik, P. / Grudnik, P. / Kolinski, M. / Zdzalik, M. / Rokita, H. / Dubin, G.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 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
H: Heavy chain of monoclonal antibody against neuroblastoma associated antigen
L: Light chain of monoclonal antibody against neuroblastoma associated antigen


Theoretical massNumber of molelcules
Total (without water)47,0002
Polymers47,0002
Non-polymers00
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-23 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.925, 46.925, 62.358
Angle α, β, γ (deg.)110.81, 92.80, 100.13
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Heavy chain of monoclonal antibody against neuroblastoma associated antigen


Mass: 22748.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Light chain of monoclonal antibody against neuroblastoma associated antigen


Mass: 24251.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Hepes, PEG 4000, isopropanol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.88563 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88563 Å / Relative weight: 1
ReflectionResolution: 1.25→57.86 Å / Num. obs: 109662 / % possible obs: 89.14 % / Redundancy: 3.8 % / Net I/σ(I): 10.99
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.71 / % possible all: 86.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementStarting model: 1f8t

1f8t


Resolution: 1.25→42.914 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1779 5515 5.03 %
Rwork0.1494 --
obs0.1508 109579 89.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→42.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 0 525 3686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053367
X-RAY DIFFRACTIONf_angle_d1.0844599
X-RAY DIFFRACTIONf_dihedral_angle_d11.591200
X-RAY DIFFRACTIONf_chiral_restr0.073526
X-RAY DIFFRACTIONf_plane_restr0.005594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26420.25021990.19523376X-RAY DIFFRACTION87
1.2642-1.27910.24611730.17813390X-RAY DIFFRACTION88
1.2791-1.29470.24381840.16813342X-RAY DIFFRACTION85
1.2947-1.31110.20811460.16613156X-RAY DIFFRACTION80
1.3111-1.32830.20371840.16043253X-RAY DIFFRACTION85
1.3283-1.34650.20311640.14913582X-RAY DIFFRACTION90
1.3465-1.36580.1962040.14893460X-RAY DIFFRACTION91
1.3658-1.38610.22011840.14833571X-RAY DIFFRACTION91
1.3861-1.40780.19791700.14543559X-RAY DIFFRACTION91
1.4078-1.43090.18481650.14383509X-RAY DIFFRACTION89
1.4309-1.45560.20742220.14293477X-RAY DIFFRACTION90
1.4556-1.4820.18171820.13683450X-RAY DIFFRACTION88
1.482-1.51050.17551790.12673385X-RAY DIFFRACTION88
1.5105-1.54140.18691610.12523108X-RAY DIFFRACTION80
1.5414-1.57490.17081820.12273367X-RAY DIFFRACTION86
1.5749-1.61150.16391730.12443642X-RAY DIFFRACTION93
1.6115-1.65180.17252030.1263553X-RAY DIFFRACTION91
1.6518-1.69650.1761960.13063582X-RAY DIFFRACTION92
1.6965-1.74640.17161860.13823556X-RAY DIFFRACTION91
1.7464-1.80280.16451870.14133532X-RAY DIFFRACTION90
1.8028-1.86720.1751740.13933449X-RAY DIFFRACTION89
1.8672-1.9420.20261730.14173230X-RAY DIFFRACTION83
1.942-2.03040.16171960.14393444X-RAY DIFFRACTION89
2.0304-2.13740.18571980.14613661X-RAY DIFFRACTION94
2.1374-2.27130.18651900.14783635X-RAY DIFFRACTION93
2.2713-2.44670.18981790.15673598X-RAY DIFFRACTION92
2.4467-2.69280.19811990.16673479X-RAY DIFFRACTION89
2.6928-3.08240.1771650.16613457X-RAY DIFFRACTION88
3.0824-3.88310.16772080.15543698X-RAY DIFFRACTION95
3.8831-42.93960.15121890.1473563X-RAY DIFFRACTION92

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