[English] 日本語
Yorodumi
- PDB-4tul: Crystal structure of monoclonal antibody against neuroblastoma as... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tul
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
  • peptide2
KeywordsIMMUNE SYSTEM / Neuroblastoma
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
Phage #D (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGolik, P. / Grudnik, P. / Dubin, G. / Zdzalik, M. / Rokita, H. / Horwacik, I.
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 24, 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy chain of monoclonal antibody against neuroblastoma associated antigen
L: Light chain of monoclonal antibody against neuroblastoma associated antigen
I: peptide2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9077
Polymers48,6343
Non-polymers2734
Water5,405300
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-42 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.676, 64.167, 78.900
Angle α, β, γ (deg.)90.00, 99.46, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein/peptide , 1 types, 1 molecules I

#3: Protein/peptide peptide2


Mass: 1633.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Phage #D (virus)

-
Antibody , 2 types, 2 molecules HL

#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)

-
Non-polymers , 3 types, 304 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MES, PEG 5000, NH4SO4 / PH range: 6.5

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→77.83 Å / Num. obs: 81806 / % possible obs: 98.96 % / Redundancy: 2 % / Rmerge(I) obs: 0.0292 / Net I/σ(I): 14.52
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 3.98 / % possible all: 99.87

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8T

1f8t


Resolution: 1.4→77.83 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.193 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21714 4103 5 %RANDOM
Rwork0.18794 ---
obs0.1894 77703 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.237 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-1.29 Å2
2---0.44 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.4→77.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 17 300 3570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.023419
X-RAY DIFFRACTIONr_bond_other_d0.0010.023112
X-RAY DIFFRACTIONr_angle_refined_deg2.2611.9574680
X-RAY DIFFRACTIONr_angle_other_deg1.00337222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2395457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75524.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45515538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4141511
X-RAY DIFFRACTIONr_chiral_restr0.1370.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
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_it1.6141.4041768
X-RAY DIFFRACTIONr_mcbond_other1.5571.4021764
X-RAY DIFFRACTIONr_mcangle_it2.2092.1012204
X-RAY DIFFRACTIONr_mcangle_other2.2092.1022205
X-RAY DIFFRACTIONr_scbond_it2.3561.5821651
X-RAY DIFFRACTIONr_scbond_other2.3551.5831652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3052.2942464
X-RAY DIFFRACTIONr_long_range_B_refined4.18812.0553818
X-RAY DIFFRACTIONr_long_range_B_other4.18912.0593819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 304 -
Rwork0.238 5772 -
obs--99.87 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more