[English] 日本語
Yorodumi
- PDB-1kip: FV MUTANT Y(B 32)A (VH DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kip
TitleFV MUTANT Y(B 32)A (VH DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 COMPLEXED WITH HEN EGG WHITE LYSOZYME
Components
  • (MONOCLONAL ANTIBODY D1.3) x 2
  • LYSOZYME
KeywordsCOMPLEX (IMMUNOGLOBULIN/HYDROLASE) / IMMUNOGLOBULIN V REGION / HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME / EGG WHITE / COMPLEX (IMMUNOGLOBULIN-HYDROLASE) / COMPLEX (IMMUNOGLOBULIN-HYDROLASE) complex
Function / homology
Function and homology information


immunoglobulin complex / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / adaptive immune response ...immunoglobulin complex / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / adaptive immune response / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
: / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Immunoglobulin V-Type ...: / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / : / Lysozyme C / Immunoglobulin kappa chain variable 12-41
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsFields, B.A. / Poljak, R.J. / Mariuzza, R.A.
Citation
Journal: Biochemistry / Year: 1996
Title: Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.
Authors: Fields, B.A. / Goldbaum, F.A. / Dall'Acqua, W. / Malchiodi, E.L. / Cauerhff, A. / Schwarz, F.P. / Ysern, X. / Poljak, R.J. / Mariuzza, R.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Bound Water Molecules and Conformational Stabilization Help Mediate an Antigen-Antibody Association
Authors: Bhat, T.N. / Bentley, G.A. / Boulot, G. / Greene, M.I. / Tello, D. / Dall'Acqua, W. / Souchon, H. / Schwarz, F.P. / Mariuzza, R.A. / Poljak, R.J.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Solvent Rearrangement in an Antigen-Antibody Interface Introduced by Site-Directed Mutagenesis of the Antibody Combining Site
Authors: Ysern, X. / Fields, B.A. / Bhat, T.N. / Goldbaum, F.A. / Dall'Acqua, W. / Schwarz, F.P. / Poljak, R.J. / Mariuzza, R.A.
History
DepositionOct 23, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: 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 / 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE 1KIP C SWS P00698 1 - 18 NOT IN ATOMS LIST

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MONOCLONAL ANTIBODY D1.3
B: MONOCLONAL ANTIBODY D1.3
C: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)38,7973
Polymers38,7973
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.230, 60.440, 56.630
Angle α, β, γ (deg.)90.00, 119.05, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody MONOCLONAL ANTIBODY D1.3


Mass: 11700.977 Da / Num. of mol.: 1 / Mutation: Y(B 32)A (VH DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: GenBank: 545862, UniProt: P01635*PLUS
#2: Antibody MONOCLONAL ANTIBODY D1.3


Mass: 12765.180 Da / Num. of mol.: 1 / Mutation: Y(B 32)A (VH DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: GenBank: 896294
#3: Protein LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell: EGG / Cellular location: EGG WHITE / Organ: EGG / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growDetails: FREE TEXT GOES HERE.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding / PH range low: 6.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-18 %(w/v)PEG80001reservoir
20.1 Mpotassium phosphate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 5, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 20023 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Num. measured all: 49442

-
Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.1→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.162 --
obs0.162 15354 70.3 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 0 116 2840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.9
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

+
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