[English] 日本語
Yorodumi
- PDB-1bvl: HUMANIZED ANTI-LYSOZYME FV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bvl
TitleHUMANIZED ANTI-LYSOZYME FV
Components(HULYS11) x 2
KeywordsHUMANIZED ANTIBODY / FV / ANTI-LYSOZYME
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsHolmes, M.A. / Foote, J.
Citation
Journal: J.Immunol. / Year: 1997
Title: Structural consequences of humanizing an antibody.
Authors: Holmes, M.A. / Foote, J.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Antibody Framework Residues Affecting the Conformation of the Hypervariable Loops
Authors: Foote, J. / Winter, G.
History
DepositionSep 16, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HULYS11
B: HULYS11
C: HULYS11
D: HULYS11


Theoretical massNumber of molelcules
Total (without water)49,6694
Polymers49,6694
Non-polymers00
Water00
1
A: HULYS11
B: HULYS11


Theoretical massNumber of molelcules
Total (without water)24,8352
Polymers24,8352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area10160 Å2
MethodPISA
2
C: HULYS11
D: HULYS11


Theoretical massNumber of molelcules
Total (without water)24,8352
Polymers24,8352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-11 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.000, 143.000, 72.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.839814, -0.234724, -0.489508), (-0.335832, 0.933082, 0.128741), (0.426533, 0.272511, -0.862443)
Vector: 143.78841, 50.8787, 6.2959)

-
Components

#1: Antibody HULYS11


Mass: 12872.358 Da / Num. of mol.: 2 / Fragment: FV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus / Genus: Homo, Mus / Species: , / Strain: , / Description: DESIGNED MOLECULE / Plasmid: LACZ/PELB / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / References: PIR: S21681
#2: Antibody HULYS11


Mass: 11962.320 Da / Num. of mol.: 2 / Fragment: FV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus / Genus: Homo, Mus / Species: , / Strain: , / Description: DESIGNED MOLECULE / Plasmid: LACZ/PELB / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / References: PIR: S21680

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.7-0.8 Msodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1994 / Details: R-AXIS IIC
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.87 Å / Num. obs: 16782 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 8.5
Reflection shellResolution: 2.87→3 Å / Mean I/σ(I) obs: 2.61 / % possible all: 83.3
Reflection
*PLUS
Num. measured all: 75768
Reflection shell
*PLUS
% possible obs: 83.3 %

-
Processing

Software
NameVersionClassification
R-AXISdata collection
R-AXISdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: 1 B-FACTOR PER RESIDUE / σ(F): 2
Details: SOME ROUNDS OF TNT REFINEMENT WERE INTERSPERSED WITH THE X-PLOR REFINEMENT.
RfactorNum. reflection% reflection
Rwork0.22 --
obs0.22 16255 93.7 %
Displacement parametersBiso mean: 23.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.87→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 0 0 3488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.9
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: 2.87→3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.293 1779 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.59 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.9

+
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