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- PDB-1jgu: STRUCTURAL BASIS FOR DISFAVORED ELIMINATION REACTION IN CATALYTIC... -

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Basic information

Entry
Database: PDB / ID: 1jgu
TitleSTRUCTURAL BASIS FOR DISFAVORED ELIMINATION REACTION IN CATALYTIC ANTIBODY 1D4
Components
  • Antibody Heavy ChainImmunoglobulin heavy chain
  • Antibody Light ChainImmunoglobulin light chain
KeywordsIMMUNE SYSTEM / IgG fold
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
Chem-HBC / HYDROXIDE ION / : / ENSMUSG00000076577 protein / Ighg protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLarsen, N.A. / Heine, A. / Crane, L. / Cravatt, B.F. / Lerner, R.A. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structural basis for a disfavored elimination reaction in catalytic antibody 1D4.
Authors: Larsen, N.A. / Heine, A. / Crane, L. / Cravatt, B.F. / Lerner, R.A. / Wilson, I.A.
History
DepositionJun 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 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
L: Antibody Light Chain
H: Antibody Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0094
Polymers47,7002
Non-polymers3082
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-27 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.37, 48.63, 69.37
Angle α, β, γ (deg.)90, 106.77, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Antibody Light Chain / Immunoglobulin light chain


Mass: 24206.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from ascites fluid / Source: (natural) Mus musculus (house mouse) / Strain: Balbc / References: GenBank: 522337, UniProt: Q52L64*PLUS
#2: Antibody Antibody Heavy Chain / Immunoglobulin heavy chain


Mass: 23493.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from ascites fluid / Source: (natural) Mus musculus (house mouse) / Strain: Balbc / References: UniProt: Q91Z05*PLUS
#3: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#4: Chemical ChemComp-HBC / (2-AMINO-3-PHENYL-BICYCLO[2.2.1]HEPT-2-YL)-PHENYL-METHANONE / BICYCLO[2.2.1]HEPTANE


Mass: 291.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4K, 10% isopropanol, 10% HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 23K
Crystal grow
*PLUS
pH: 5.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein11
20.2 Msodium acetate11pH5.5
318-21 %(w/v)PEG400012
40.1 Misopropanol12
50.1 MHEPES12pH7.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 40444 / Num. obs: 40444 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 14
Reflection shellHighest resolution: 1.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.493 / % possible all: 99

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.229 20222 RANDOM
Rwork0.209 --
all0.209 40770 -
obs0.209 40444 -
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 23 330 3707
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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