[English] 日本語
Yorodumi
- PDB-1it9: CRYSTAL STRUCTURE OF AN ANTIGEN-BINDING FRAGMENT FROM A HUMANIZED... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1it9
TitleCRYSTAL STRUCTURE OF AN ANTIGEN-BINDING FRAGMENT FROM A HUMANIZED VERSION OF THE ANTI-HUMAN FAS ANTIBODY HFE7A
Components
  • HUMANIZED ANTIBODY HFE7A, HEAVY CHAIN
  • HUMANIZED ANTIBODY HFE7A, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / ANTI_FAS / AGONISTIC_ANTIBODY / APOPTOSIS / ANTIBODY_HUMANIZATION
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsIto, S. / Takayama, T. / Hanzawa, H. / Takahashi, T. / Miyadai, K. / Serizawa, N. / Hata, T. / Haruyama, H.
Citation
Journal: BIOL.PHARM.BULL. / Year: 2002
Title: Humanization of the Mouse Anti-Fas Antibody HFE7A and Crystal Structure of the Humanized HFE7A Fab Fragment
Authors: Haruyama, H. / Ito, S. / Miyadai, K. / Takahashi, T. / Kawaida, R. / Takayama, T. / Hanzawa, H. / Hata, T. / Yamaguchi, J. / Yoshida-Kato, H. / Ichikawa, K. / Ohsumi, J. / Yonehara, S. / Serizawa, N.
#1: Journal: To be Published
Title: CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF THE FAB FRAGMENT FROM A HUMANIZED VERSION OF THE MOUSE ANTI-HUMAN FAS ANTIBODY HFE7A
Authors: Ito, S. / Takayama, T. / Hanzawa, H. / Takahashi, T. / Miyadai, K. / Serizawa, N. / Haruyama, H. / Hata, T.
#2: Journal: J.BIOCHEM.(TOKYO) / Year: 2002
Title: Crystal Structure of the Antigen-Binding Fragment of Apoptosis-Inducing Mouse Anti-Human Fas Monoclonal Antibody HFE7A
Authors: Ito, S. / Takayama, T. / Hanzawa, H. / Ichikawa, K. / Ohsumi, J. / Serizawa, N. / Hata, T. / Haruyama, H.
History
DepositionJan 11, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2019Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_description ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 10, 2024Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_genus

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: HUMANIZED ANTIBODY HFE7A, LIGHT CHAIN
H: HUMANIZED ANTIBODY HFE7A, HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,0952
Polymers47,0952
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-18 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.365, 82.746, 104.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody HUMANIZED ANTIBODY HFE7A, LIGHT CHAIN


Mass: 23501.871 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species: , / Strain: , / Description: humanized mouse / Plasmid: pEE / Cell line (production host): cos-1 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q6GMV9
#2: Antibody HUMANIZED ANTIBODY HFE7A, HEAVY CHAIN


Mass: 23593.266 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species: , / Strain: , / Description: humanized mouse / Plasmid: pEE / Cell line (production host): cos-1 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q6PJA4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, SODIUM ACETATE, METHANOL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %PEG40001reservoir
20.1 Msodium acetate1reservoirpH4.6
330 %methanol1reservoir

-
Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12285 / % possible obs: 90.7 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 5.4 / % possible all: 77.1
Reflection
*PLUS
Num. obs: 11136 / % possible obs: 91 % / Num. measured all: 61689 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 71.3 % / Num. unique obs: 927 / Num. measured obs: 3790 / Rmerge(I) obs: 0.18

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1144 10.3 %RANDOM
Rwork0.202 ---
obs0.202 11089 91 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 0 6 3319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.841.5
X-RAY DIFFRACTIONx_mcangle_it4.592
X-RAY DIFFRACTIONx_scbond_it4.32
X-RAY DIFFRACTIONx_scangle_it6.062.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 178 12.7 %
Rwork0.242 1399 -
obs--79.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 9 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.55

+
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