[English] 日本語
Yorodumi
- PDB-1h3p: STRUCTURAL CHARACTERISATION OF A MONOCLONAL ANTIBODY SPECIFIC FOR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h3p
TitleSTRUCTURAL CHARACTERISATION OF A MONOCLONAL ANTIBODY SPECIFIC FOR THE PRES1 REGION OF THE HEPATITIS B VIRUS
Components(ANTIBODY FAB FRAGMENT) x 2
KeywordsIMMUNOGLOBULIN / ANTIBODY FAB FRAGMENT
Function / homology
Function and homology information


immune response / extracellular space / metal ion binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ENSMUSG00000076577 protein / VH7183-DSP2-JH3-CH1 protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPizarro, J.C. / Vulliez-Le-normand, B. / Riottot, M.M. / Budkowska, A. / Bentley, G.A.
CitationJournal: FEBS Lett. / Year: 2001
Title: Structural and Functional Characterisation of a Monoclonal Antibody Specific for the Pres1 Region of Hepatitis B Virus
Authors: Pizarro, J.C. / Vulliez-Le-Normand, B. / Riottot, M.M. / Budkowska, A. / Bentley, G.A.
History
SupersessionSep 12, 2002ID: 1GM3
DepositionSep 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: ANTIBODY FAB FRAGMENT
L: ANTIBODY FAB FRAGMENT


Theoretical massNumber of molelcules
Total (without water)49,8112
Polymers49,8112
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.010, 88.460, 111.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE DIMER IS A HETERODIMER FORMED BY ONE FAB LIGHTCHAIN AND ONE FAB HEAVY CHAIN.

-
Components

#1: Antibody ANTIBODY FAB FRAGMENT


Mass: 23505.330 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: 5A19 HYBRIDOME / Strain: BALB/C / References: UniProt: Q65ZL8*PLUS
#2: Antibody ANTIBODY FAB FRAGMENT


Mass: 26305.312 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: 5A19 HYBRIDOME / Strain: BALB/C / References: UniProt: Q52L64*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growpH: 8.5
Details: 0.1M CYSTEINE, 15% PEG6000, 110MM MGCL2, 60MM TRISHCL PH8.5, 15% GLYCEROL, pH 8.50
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 Mcysteine1reservoir
215 %(w/v)PEG60001reservoir
3110 mM1reservoirMgCl2
460 mMTris-HCl1reservoirpH8.5
515 %glycerol1reservoir
64.7 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 14823 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 6 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 5.6 / % possible all: 88
Reflection
*PLUS
Lowest resolution: 15 Å / Rmerge(I) obs: 0.077

-
Processing

Software
NameVersionClassification
X-PLOR3.581refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H1L
Resolution: 2.6→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUE NUMBERING FOLLOWS THE KABAT CONVENTION (E.A.KABAT,T.T.WU, M.REID-MILLER, H.M.PERRY, A K.S.GOTTESMAN (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGIC INTEREST, 5TH ED., NATIONAL INSTITUTES ...Details: RESIDUE NUMBERING FOLLOWS THE KABAT CONVENTION (E.A.KABAT,T.T.WU, M.REID-MILLER, H.M.PERRY, A K.S.GOTTESMAN (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGIC INTEREST, 5TH ED., NATIONAL INSTITUTES OF HEALTH BETHESDA RESIDUES H129-H132 AND THE LAST TWO RESIDUES OF BOTH HEAVY AND LIGHT CHAINS WERE MODELLED USING STEREOCHEMICAL RESTRAINTS ONLY. RESIDUE H98 HAS MULTIPLE CONFORMATIONS. RESIDUES WITH WEAK DENSITY INDICATION HAVE 0 OCCUPANCY. THESE RESIDUES HAVE BEEN LISTED IN REMARK 465 AND REMARK 470
RfactorNum. reflection% reflectionSelection details
Rfree0.2908 741 5 %RANDOM
Rwork0.2126 ---
obs0.2126 14559 98 %-
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 0 132 3440
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
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: 2.6→2.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.474 74 4.99 %
Rwork0.324 1134 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6

+
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