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- PDB-1pkq: Myelin Oligodendrocyte Glycoprotein-(8-18C5) Fab-complex -

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Basic information

Entry
Database: PDB / ID: 1pkq
TitleMyelin Oligodendrocyte Glycoprotein-(8-18C5) Fab-complex
Components
  • (8-18C5) chimeric Fab, heavy chain
  • (8-18C5) chimeric Fab, light chain
  • Myelin Oligodendrocyte Glycoprotein
KeywordsIMMUNE SYSTEM / autoantibody / multiple sclerosis / EAE
Function / homology
Function and homology information


response to folic acid / response to lipid / regulation of cytokine production / T cell receptor signaling pathway / cell adhesion / signaling receptor binding / external side of plasma membrane / cell surface
Similarity search - Function
Myelin-oligodendrocyte glycoprotein / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Myelin-oligodendrocyte glycoprotein / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Myelin-oligodendrocyte glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBreithaupt, C. / Schubart, A. / Zander, H. / Skerra, A. / Huber, R. / Linington, C. / Jacob, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structural insights into the antigenicity of myelin oligodendrocyte glycoprotein
Authors: Breithaupt, C. / Schubart, A. / Zander, H. / Skerra, A. / Huber, R. / Linington, C. / Jacob, U.
History
DepositionJun 6, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (8-18C5) chimeric Fab, light chain
B: (8-18C5) chimeric Fab, heavy chain
E: Myelin Oligodendrocyte Glycoprotein
F: (8-18C5) chimeric Fab, light chain
G: (8-18C5) chimeric Fab, heavy chain
J: Myelin Oligodendrocyte Glycoprotein


Theoretical massNumber of molelcules
Total (without water)137,5326
Polymers137,5326
Non-polymers00
Water1,53185
1
A: (8-18C5) chimeric Fab, light chain
B: (8-18C5) chimeric Fab, heavy chain
E: Myelin Oligodendrocyte Glycoprotein


Theoretical massNumber of molelcules
Total (without water)68,7663
Polymers68,7663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: (8-18C5) chimeric Fab, light chain
G: (8-18C5) chimeric Fab, heavy chain
J: Myelin Oligodendrocyte Glycoprotein


Theoretical massNumber of molelcules
Total (without water)68,7663
Polymers68,7663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.480, 40.000, 134.200
Angle α, β, γ (deg.)90.00, 107.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody (8-18C5) chimeric Fab, light chain


Mass: 26154.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ig light chain / Plasmid: pASK107 / Production host: Escherichia coli (E. coli)
#2: Antibody (8-18C5) chimeric Fab, heavy chain


Mass: 26683.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ig heavy chain / Plasmid: pASK107 / Production host: Escherichia coli (E. coli)
#3: Protein Myelin Oligodendrocyte Glycoprotein


Mass: 15928.754 Da / Num. of mol.: 2 / Fragment: N-terminal Ig domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: MOG / Plasmid: pQE12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63345
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris/HCl, MOPS, NaCl, PEG8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13.5 mg/mlprotein1drop
25 mMMOPS1droppH7.5
350 mM1dropNaCl
4100 mMTris-HCl1reservoirpH8.5
514 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2002
RadiationMonochromator: Si(111) double crystal, non dispersive / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 3→18 Å / Num. obs: 22442 / % possible obs: 86.7 % / Redundancy: 2.3 % / Biso Wilson estimate: 69.1 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 5.3
Reflection shellResolution: 3→3.09 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2 / Num. unique all: 1590 / % possible all: 73
Reflection
*PLUS
Num. obs: 22490
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 73 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoRE& BEASTphasing
CNSrefinement
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→18 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.319 1091 -random
Rwork0.25 ---
all-22437 --
obs-21346 86 %-
Displacement parametersBiso mean: 33.6 Å2
Refinement stepCycle: LAST / Resolution: 3→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8432 0 0 85 8517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.66
LS refinement shellResolution: 3→3.05 Å /
RfactorNum. reflection
Rfree0.387 38
Rwork0.351 -
obs-923
Refinement
*PLUS
Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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