[English] 日本語
Yorodumi
- PDB-2iqa: PFA2 FAB fragment, monoclinic apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iqa
TitlePFA2 FAB fragment, monoclinic apo form
Components(IgG2a Fab fragment PFA2 ...) x 2
KeywordsIMMUNE SYSTEM / pfa2 / wwddd / cdr
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / 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
ACETAMIDE / If kappa light chain / Anti-human Fc gamma receptor III 3G8 gamma heavy chain variable region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGardberg, A.S. / Dealwis, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular basis for passive immunotherapy of Alzheimer's disease
Authors: Gardberg, A.S. / Dice, L.T. / Ou, S. / Rich, R.L. / Helmbrecht, E. / Ko, J. / Wetzel, R. / Myszka, D.G. / Patterson, P.H. / Dealwis, C.
History
DepositionOct 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Presently, there is no aminoacid sequence database reference available for the two ...SEQUENCE Presently, there is no aminoacid sequence database reference available for the two proteins IGG2A FAB fragment heavy chain and IGG2A FAB fragment light chain kappa

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: IgG2a Fab fragment PFA2 Kappa light chain
H: IgG2a Fab fragment PFA2 heavy chain
A: IgG2a Fab fragment PFA2 Kappa light chain
B: IgG2a Fab fragment PFA2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,99215
Polymers96,1024
Non-polymers89011
Water4,900272
1
L: IgG2a Fab fragment PFA2 Kappa light chain
H: IgG2a Fab fragment PFA2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5148
Polymers48,0512
Non-polymers4636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-38 kcal/mol
Surface area19470 Å2
MethodPISA, PQS
2
A: IgG2a Fab fragment PFA2 Kappa light chain
B: IgG2a Fab fragment PFA2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4787
Polymers48,0512
Non-polymers4275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-27 kcal/mol
Surface area19740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.984, 73.412, 93.508
Angle α, β, γ (deg.)90.00, 99.97, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterodimer.

-
Components

-
Antibody , 2 types, 4 molecules LAHB

#1: Antibody IgG2a Fab fragment PFA2 Kappa light chain


Mass: 24146.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: A2NHM3
#2: Antibody IgG2a Fab fragment PFA2 heavy chain


Mass: 23903.994 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: Q811U5

-
Non-polymers , 4 types, 283 molecules

#3: Chemical ChemComp-ACM / ACETAMIDE / Acetamide


Mass: 59.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growMethod: vapor diffusion / pH: 6.5
Details: 0.1 M Bis-Tris, 28% PEG-MME 2000, pH 6.5, VAPOR DIFFUSION

-
Data collection

Diffraction
IDCrystal-ID
11
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2→33.45 Å / Num. obs: 70368 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.09 / Net I/σ(I): 22.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.26 / Num. unique all: 6934 / Rsym value: 0.405 / % possible all: 99.4

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
BIO-CARSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IQ9

2iq9


Resolution: 2→33.45 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.731 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3567 5.1 %RANDOM
Rwork0.23 ---
obs0.232 70337 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-2.18 Å2
2--1.28 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 2→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 0 57 272 7025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226951
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9589471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1315885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22724.1261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9341528
X-RAY DIFFRACTIONr_chiral_restr0.0950.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025176
X-RAY DIFFRACTIONr_nbd_refined0.2040.22798
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2345
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.215
X-RAY DIFFRACTIONr_mcbond_it0.8161.54502
X-RAY DIFFRACTIONr_mcangle_it1.37127129
X-RAY DIFFRACTIONr_scbond_it1.732846
X-RAY DIFFRACTIONr_scangle_it2.544.52335
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 257 -
Rwork0.291 4835 -
obs-5092 97.16 %

+
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