[English] 日本語
Yorodumi
- PDB-1b2w: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF A HUMANIZED AND... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b2w
TitleCOMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF A HUMANIZED AND A CHIMERIC FAB OF AN ANTI-GAMMA-INTERFERON ANTIBODY
Components
  • PROTEIN (ANTIBODY (HEAVY CHAIN))
  • PROTEIN (ANTIBODY (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / ANTIBODY ENGINEERING / HUMANIZED AND CHIMERIC ANTIBODY / FAB / THREE-DIMENSIONAL STRYCTURE / GAMMA-INTERFERON
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFan, Z. / Shan, L. / Goldsteen, B.Z. / Guddat, L.W. / Thakur, A. / Landolfi, N.F. / Co, M.S. / Vasquez, M. / Queen, C. / Ramsland, P.A. / Edmundson, A.B.
CitationJournal: J.Mol.Recog. / Year: 1999
Title: Comparison of the three-dimensional structures of a humanized and a chimeric Fab of an anti-gamma-interferon antibody.
Authors: Fan, Z.C. / Shan, L. / Goldsteen, B.Z. / Guddat, L.W. / Thakur, A. / Landolfi, N.F. / Co, M.S. / Vasquez, M. / Queen, C. / Ramsland, P.A. / Edmundson, A.B.
History
DepositionDec 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2014Group: Source and taxonomy
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 9, 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 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: PROTEIN (ANTIBODY (LIGHT CHAIN))
H: PROTEIN (ANTIBODY (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)47,2322
Polymers47,2322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-28 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.100, 74.600, 104.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody PROTEIN (ANTIBODY (LIGHT CHAIN)) / IMMUNOGLOBULIN


Mass: 23430.879 Da / Num. of mol.: 1 / Fragment: V DOMAIN AND C DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens
#2: Antibody PROTEIN (ANTIBODY (HEAVY CHAIN)) / IMMUNOGLOBULIN


Mass: 23800.799 Da / Num. of mol.: 1 / Fragment: V DOMAIN AND C DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.2
Details: 6.6% PEG 8000(W/V), IN 0.05 M NACL AND 0.05% SODIUM AZIDE., pH 6.2
Components of the solutions
IDNameCrystal-IDSol-ID
16.6% PEG 8000(W/V)12
20.05 M NACL12
30.05% SODIUM AZIDE12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18-20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135-45 mg/mlprotein1drop
26.6 %(w/v)PEG80001reservoir
30.05 M1reservoirNaCl
40.05 %sodium azide1reservoir

-
Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1994
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.79→20 Å / Num. obs: 11491 / % possible obs: 81.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 8.3
Reflection shellResolution: 2.79→2.96 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1 / Rsym value: 0.41 / % possible all: 0.28
Reflection
*PLUS
% possible obs: 67.2 %

-
Processing

Software
NameVersionClassification
X-GENdata reduction
X-PLORmodel building
X-PLOR3.8refinement
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFB

1dfb


Resolution: 2.9→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.33 897 10 %RANDOM
Rwork0.188 ---
obs-9440 67.6 %-
Displacement parametersBiso mean: 30 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 0 3325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 51 3.6 %
Rwork0.26 372 -
obs--29.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PCA.PARPCA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.331
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

+
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