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- PDB-1r70: Model of human IgA2 determined by solution scattering, curve fitt... -

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Basic information

Entry
Database: PDB / ID: 1r70
TitleModel of human IgA2 determined by solution scattering, curve fitting and homology modelling
Components
  • Human IgA2(m1) Heavy Chain
  • Human IgA2(m1) Light Chain
KeywordsIMMUNE SYSTEM / Immunology / antibody / IgA / glycoprotein / Ig fold
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / SYNCHROTRON / NUCLEAR REACTOR / CONSTRAINED MODEL FIT / Resolution: 30 Å
AuthorsFurtado, P.B. / Whitty, P.W. / Robertson, A. / Eaton, J.T. / Almogren, A. / Kerr, M.A. / Woof, J.M. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution Structure Determination of Monomeric Human IgA2 by X-ray and Neutron Scattering, Analytical Ultracentrifugation and Constrained Modelling: A Comparison with Monomeric Human IgA1.
Authors: Furtado, P.B. / Whitty, P.W. / Robertson, A. / Eaton, J.T. / Almogren, A. / Kerr, M.A. / Woof, J.M. / Perkins, S.J.
History
DepositionOct 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Apr 25, 2018Group: Data collection / Category: diffrn_radiation / diffrn_source
Item: _diffrn_radiation.pdbx_scattering_type / _diffrn_source.source
Revision 1.5Jun 13, 2018Group: Data collection / Category: diffrn_radiation
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE At the time of processing, there were no suitable sequence database references for the ...SEQUENCE At the time of processing, there were no suitable sequence database references for the proteins in this entry.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Human IgA2(m1) Light Chain
B: Human IgA2(m1) Heavy Chain
C: Human IgA2(m1) Light Chain
D: Human IgA2(m1) Heavy Chain


Theoretical massNumber of molelcules
Total (without water)146,2784
Polymers146,2784
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody Human IgA2(m1) Light Chain / Coordinate model: Cα atoms only


Mass: 23216.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: human alpha 2 gene (light chain) / Plasmid: pEE6.HCMV / Cell line (production host): Chinese hamster ovary (CHO) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1
#2: Antibody Human IgA2(m1) Heavy Chain / Coordinate model: Cα atoms only


Mass: 49922.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: human alpha 2 gene (heavy chain) / Plasmid: pEE6.HCMV / Cell line (production host): Chinese hamster ovary (CHO) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
22881
32881
Diffraction source
SourceSiteBeamlineTypeID
SYNCHROTRONSRS SRS BEAMLINE1
SYNCHROTRONESRF ID22
NUCLEAR REACTORISIS INSTRUMENT LOQ3
Detector
TypeIDDetectorDate
500 CHANNEL1QUADRANT DETECTORSep 15, 2000
FReLoN2CCDJul 15, 2002
WIRE DETECTOR33HE ORDELANov 15, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystalSINGLE WAVELENGTHMx-ray1
2single crystalSINGLE WAVELENGTHMx-ray1
3time-of-flightLAUELneutron1
Radiation wavelengthRelative weight: 1
Soln scatter

Data analysis software list: SCTPL7, GNOM / Sample pH: 7.4 / Temperature: 288 K

TypeIDBuffer nameConc. range (mg/ml)Data reduction software listDetector typeMax mean cross sectional radii gyration (nm)Max mean cross sectional radii gyration esd (nm)Mean guiner radius (nm)Mean guiner radius esd (nm)Min mean cross sectional radii gyration (nm)Min mean cross sectional radii gyration esd (nm)Num. of time framesProtein lengthSource beamlineSource classSource typeSource beamline instrument
x-ray1DULBECCO PBS2-15OTOKO500-CHANNEL QUADRANT1.370.165.170.112.390.11012.1YSRS BEAMLINE 2.1
x-ray2DULBECCO PBS0.55-1.12MULTICCDFRELON CCD CAMERA1.470.085.180.092.470.091016ID02YESRF BEAMLINE ID02
neutron3PBS IN 99.9% D2O2.0-3.0COLLETTEAREA (TIME-OF-FLIGHT)1.040.065.030.012.210.11PULSED NEUTRONNISISLOQ

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Processing

Software
NameVersionClassification
DETECTORdata collection
OTOKOdata reduction
COLLETTEdata reduction
SCTPL5model building
SCTPL7model building
GNOMmodel building
Insight IIIImodel building
DISCOVERrefinement
Omodel building
DETECTORSUPPLIED SOFTWAREdata reduction
OTOKOdata scaling
COLLETTEdata scaling
SCTPLVERSION 5phasing
GNOMphasing
RefinementMethod to determine structure: CONSTRAINED MODEL FIT / Resolution: 30→1300 Å / Rfactor all: 0.066 / Stereochemistry target values: ENGH & HUBER
Refinement stepCycle: LAST / Resolution: 30→1300 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 0 1352
Soln scatter modelMethod: CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS
Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN ...Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT R-FACTOR DEFINED BY ANALOGY WITH PROTEIN CRYSTALLOGRAPHY AND BASED ON THE EXPERIMENTAL CURVES IN THE Q RANGE EXTENDING TO 2.2 NM-1 (ESRF X-RAYS) AND 2.2 NM-1 (ISIS NEUTRONS).
Details: HOMOLOGY MODELS WERE BUILT FOR THE IGA2 FAB AND FC FRAGMENTS STARTING FROM THE IGA1 MODEL (PDB ENTRY 1IGA). THE POSITIONS OF THE FAB FRAGMENTS RELATIVE TO THE FC FRAGMENT WERE DETERMINED BY ...Details: HOMOLOGY MODELS WERE BUILT FOR THE IGA2 FAB AND FC FRAGMENTS STARTING FROM THE IGA1 MODEL (PDB ENTRY 1IGA). THE POSITIONS OF THE FAB FRAGMENTS RELATIVE TO THE FC FRAGMENT WERE DETERMINED BY AN APPROACH THAT COMBINED RANDOM HINGE PEPTIDE STRUCTURES PRODUCED BY MOLECULAR DYNAMICS SIMULATIONS WITH CURVE-FITTING TO EXPERIMENTAL SOLUTION SCATTERING DATA. THE X-RAY AND NEUTRON SCATTERING CURVE I(Q) WAS CALCULATED ASSUMING A UNIFORM SCATTERING DENSITY FOR THE SPHERES USING THE DEBYE EQUATION AS ADAPTED TO SPHERES. X-RAY CURVES WERE CALCULATED FROM THE HYDRATED SPHERE MODELS WITHOUT CORRECTIONS FOR WAVELENGTH SPREAD OR BEAM DIVERGENCE, WHILE THESE CORRECTIONS WERE APPLIED FOR THE NEUTRON CURVES BUT NOW USING UNHYDRATED MODELS. A SINGLE ARRANGEMENT OF THE FAB FRAGMENTS IS PRESENTED, WHICH IS REPRESENTATIVE OF A FAMILY OF STRUCTURES THAT FIT THE SCATTERING DATA. MORE DETAILS ON THE MODELLING STRATEGY ARE CONTAINED IN THE PRIMARY REFERENCE.
Num. of conformers calculated: 10000 / Num. of conformers submitted: 1 / Representative conformer: 1 / Software author list: ACCELRYS
Software list: INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI, O, SCTPL7, GNOM

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