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- PDB-1dn0: STRUCTURE OF THE FAB FRAGMENT FROM A HUMAN IGM COLD AGGLUTININ -

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Basic information

Entry
Database: PDB / ID: 1dn0
TitleSTRUCTURE OF THE FAB FRAGMENT FROM A HUMAN IGM COLD AGGLUTININ
Components
  • IGM-KAPPA COLD AGGLUTININ (HEAVY CHAIN)
  • IGM-KAPPA COLD AGGLUTININ (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / FAB / IGM / ANTIBODY / COLD AGGLUTININ / HUMAN
Function / homology
Function and homology information


immune response / extracellular space
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
: / : / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.28 Å
AuthorsCauerhff, A. / Braden, B. / Carvalho, J.G. / Leoni, J. / Polikarpov, I. / Goldbaum, F.
CitationJournal: J.Immunol. / Year: 2000
Title: Three-dimensional structure of the Fab from a human IgM cold agglutinin.
Authors: Cauerhff, A. / Braden, B.C. / Carvalho, J.G. / Aparicio, R. / Polikarpov, I. / Leoni, J. / Goldbaum, F.A.
History
DepositionDec 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGM-KAPPA COLD AGGLUTININ (LIGHT CHAIN)
B: IGM-KAPPA COLD AGGLUTININ (HEAVY CHAIN)
C: IGM-KAPPA COLD AGGLUTININ (LIGHT CHAIN)
D: IGM-KAPPA COLD AGGLUTININ (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)96,8724
Polymers96,8724
Non-polymers00
Water11,061614
1
A: IGM-KAPPA COLD AGGLUTININ (LIGHT CHAIN)
B: IGM-KAPPA COLD AGGLUTININ (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)48,4362
Polymers48,4362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-23 kcal/mol
Surface area19150 Å2
MethodPISA
2
C: IGM-KAPPA COLD AGGLUTININ (LIGHT CHAIN)
D: IGM-KAPPA COLD AGGLUTININ (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)48,4362
Polymers48,4362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-24 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.880, 110.880, 170.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11D-2239-

HOH

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Components

#1: Antibody IGM-KAPPA COLD AGGLUTININ (LIGHT CHAIN)


Mass: 23301.770 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: PIR: A23746, UniProt: Q6PJF2*PLUS
#2: Antibody IGM-KAPPA COLD AGGLUTININ (HEAVY CHAIN)


Mass: 25134.043 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: PIR: B23746
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O

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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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17%PEG 8,000, 0.1M NA HEPES., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Temperature: 25 ℃ / Details: Cauerhff, A., (1998) Protein Pept.Lett., 5, 177.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
214 %(w/w)PEG80001reservoir
30.1 Msodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.3
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionHighest resolution: 2.28 Å / Num. all: 56015 / Num. obs: 50825 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.28→2.3 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.28→100 Å / σ(F): 0 / σ(I): 1
RfactorNum. reflection
Rfree0.24 -
Rwork0.18 -
obs0.18 50825
all-56015
Refinement stepCycle: LAST / Resolution: 2.28→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6594 0 0 614 7208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / Rfactor obs: 0.18 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.023

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