[English] 日本語
Yorodumi
- PDB-8fab: CRYSTAL STRUCTURE OF THE FAB FRAGMENT FROM THE HUMAN MYELOMA IMMU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fab
TitleCRYSTAL STRUCTURE OF THE FAB FRAGMENT FROM THE HUMAN MYELOMA IMMUNOGLOBULIN IGG HIL AT 1.8 ANGSTROMS RESOLUTION
Components
  • IGG1-LAMBDA HIL FAB (HEAVY CHAIN)
  • IGG1-LAMBDA HIL FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSaul, F.A. / Poljak, R.J.
Citation
Journal: Biochemistry / Year: 1991
Title: Three-dimensional structure of murine anti-p-azophenylarsonate Fab 36-71. 1. X-ray crystallography, site-directed mutagenesis, and modeling of the complex with hapten.
Authors: Strong, R.K. / Campbell, R. / Rose, D.R. / Petsko, G.A. / Sharon, J. / Margolies, M.N.
#1: Journal: Biochemistry / Year: 1979
Title: Amino Acid Sequence of the VH Region of Human Myeloma Cryoimmunoglobulin Igg Hil
Authors: Chiu, Y.-Y.H. / Lopez De Castro, J.A. / Poljak, R.J.
#2: Journal: Biochemistry / Year: 1978
Title: Amino Acid Sequence of the Variable Region of the Light (Lambda) Chain from Human Myeloma Cryoimmunoglobulin Igg Hil
Authors: Lopez De Castro, J.A. / Chiu, Y.-Y.H. / Poljak, R.J.
#3: Journal: Nature / Year: 1969
Title: Crystals of Fragment Fab': Preparation from Pepsin Digests of Human Igg Myeloma Proteins
Authors: Rossi, G. / Choi, T.K. / Nisonoff, A.
History
DepositionMar 23, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IGG1-LAMBDA HIL FAB (LIGHT CHAIN)
B: IGG1-LAMBDA HIL FAB (HEAVY CHAIN)
C: IGG1-LAMBDA HIL FAB (LIGHT CHAIN)
D: IGG1-LAMBDA HIL FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)93,7154
Polymers93,7154
Non-polymers00
Water12,034668
1
A: IGG1-LAMBDA HIL FAB (LIGHT CHAIN)
B: IGG1-LAMBDA HIL FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8572
Polymers46,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-20 kcal/mol
Surface area19100 Å2
MethodPISA
2
C: IGG1-LAMBDA HIL FAB (LIGHT CHAIN)
D: IGG1-LAMBDA HIL FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8572
Polymers46,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-23 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.600, 127.420, 66.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE 141 IN CHAINS *A* AND *C* ARE CIS PROLINES.
2: RESIDUES 155 AND 157 IN CHAINS *B* AND *D* ARE CIS PROLINES.

-
Components

#1: Antibody IGG1-LAMBDA HIL FAB (LIGHT CHAIN)


Mass: 22767.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: PIR: S25738
#2: Antibody IGG1-LAMBDA HIL FAB (HEAVY CHAIN)


Mass: 24090.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: EMBL: Y14737
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN THE SEQUENCE DATA BASE, THE SEQUENCE FOR THE HEAVY CHAIN IS INCOMPLETE AND THE SEQUENCE FOR THE ...IN THE SEQUENCE DATA BASE, THE SEQUENCE FOR THE HEAVY CHAIN IS INCOMPLETE AND THE SEQUENCE FOR THE LIGHT CHAIN IS NON-EXISTENT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal grow
*PLUS
Method: vapor diffusion
Details: referred to 'Rose,D.R.', (1990) Proc.Natl.Acad.Sci.U.S.A., 87, 338-342
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114.9 %(w/w)PEG80001drop
24.0 mg/mlprotein1drop
350 mMphosphate1drop
40.5 %(w/w)1dropNaN3
58.5 %PEG80001reservoir
650 mMpotassium phosphate1reservoir
70.5 %1reservoirNaN3

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→6 Å / σ(F): 2.5 /
RfactorNum. reflection
Rwork0.173 -
obs0.173 64477
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6405 0 0 668 7073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.96
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 64477 / σ(F): 2.5 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.96

+
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