[English] 日本語
Yorodumi
- PDB-1yuh: FAB FRAGMENT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yuh
TitleFAB FRAGMENT
Components
  • 88C6/12 FAB (HEAVY CHAIN)
  • 88C6/12 FAB (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / ANTI-NITROPHENOL / LAMBDA LIGHT CHAIN / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-NP / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsYuhasz, S.C. / Amzel, L.M. / Parry, C. / Strand, M.
Citation
Journal: Mol.Immunol. / Year: 1995
Title: Structural analysis of affinity maturation: the three-dimensional structures of complexes of an anti-nitrophenol antibody.
Authors: Yuhasz, S.C. / Parry, C. / Strand, M. / Amzel, L.M.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization and Preliminary X-Ray Diffraction Studies of an Anti-4-Hydroxy-3-Nitrophenylacetic Acid Monoclonal Antibody Fab Fragment Complexed with Immunizing and Heteroclitic Haptens
Authors: Yuhasz, S.C. / Ysern, X. / Strand, M. / Amzel, L.M.
History
DepositionJan 30, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Source and taxonomy
Revision 1.4Mar 21, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.pdbx_collection_date / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: 88C6/12 FAB (LIGHT CHAIN)
H: 88C6/12 FAB (HEAVY CHAIN)
A: 88C6/12 FAB (LIGHT CHAIN)
B: 88C6/12 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8346
Polymers92,2134
Non-polymers6212
Water724
1
L: 88C6/12 FAB (LIGHT CHAIN)
H: 88C6/12 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4173
Polymers46,1072
Non-polymers3101
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-20 kcal/mol
Surface area19250 Å2
MethodPISA
2
A: 88C6/12 FAB (LIGHT CHAIN)
B: 88C6/12 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4173
Polymers46,1072
Non-polymers3101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-22 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.200, 86.900, 131.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody 88C6/12 FAB (LIGHT CHAIN)


Mass: 22672.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 387376
#2: Antibody 88C6/12 FAB (HEAVY CHAIN)


Mass: 23434.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 3399661
#3: Chemical ChemComp-NP / 4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACID


Mass: 310.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N2O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - ...IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - 109, CL1 110 - 212 AND THE HEAVY CHAIN RESIDUES ARE VH1 1 - 117, CH1 118 - 218, RESPECTIVELY. MOLECULE 2 DEFINES THE LIGHT CHAIN RESIDUES AS VL2 2 - 109, CL2 110 - 212, AND HEAVY CHAIN RESIDUES AS VH2 1 - 117 AND CH2 118 - 218, RESPECTIVELY. THE WATERS ARE NUMBERED 990 - 994 AND THE 2 NITROPHENOL-EPSILON-AMINO CAPROIC MOLECULES LABELED AS NP ARE NUMBERED 995 AND 996.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal grow
*PLUS
pH: 6.52 / Method: vapor diffusion, hanging drop / Details: Yuhasz, S.C., (1989) J.Mol.Biol., 209, 319.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 mg/mlFab1drop
220 mMsodium phosphate1reservoir
332 %(w/v)PEG34001reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 16470 / % possible obs: 70.3 % / Rmerge(I) obs: 0.047
Reflection
*PLUS
Highest resolution: 3 Å

-
Processing

Software
NameClassification
XENGENdata collection
X-PLORrefinement
XENGENdata reduction
RefinementResolution: 3→6 Å / σ(F): 2
Details: IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - 109, CL1 110 - 212 AND THE HEAVY CHAIN RESIDUES ARE VH1 1 - 117, CH1 118 - 218, RESPECTIVELY. ...Details: IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - 109, CL1 110 - 212 AND THE HEAVY CHAIN RESIDUES ARE VH1 1 - 117, CH1 118 - 218, RESPECTIVELY. MOLECULE 2 DEFINES THE LIGHT CHAIN RESIDUES AS VL2 2 - 109, CL2 110 - 212, AND HEAVY CHAIN RESIDUES AS VH2 1 - 117 AND CH2 118 - 218, RESPECTIVELY. THE WATERS ARE NUMBERED 990 - 994 AND THE 2 NITROPHENOL-EPSILON-AMINO CAPROIC MOLECULES LABELED AS NP ARE NUMBERED 995 AND 996. RESIDUES NUMBERED 132 - 140 OF H AND B CHAINS WERE NOT FOUND IN THE ELECTRON DENSITY AND ARE PROBABLY DISORDERED.
RfactorNum. reflection
Rwork0.19 -
obs0.19 10275
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 44 4 6530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg4.08
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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