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

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Basic information

Entry
Database: PDB / ID: 1jgv
TitleSTRUCTURAL BASIS FOR DISFAVORED ELIMINATION REACTION IN CATALYTIC ANTIBODY 1D4
Components
  • Antibody Heavy Chain
  • Antibody Light Chain
KeywordsIMMUNE SYSTEM / IgG fold
Function / homology
Function and homology information


: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / ENSMUSG00000076577 protein / Ighg protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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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


Theoretical massNumber of molelcules
Total (without water)47,8582
Polymers47,8582
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-26 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.65, 48.17, 69.28
Angle α, β, γ (deg.)90, 106.20, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Antibody Light Chain


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


Mass: 23650.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from IgG derived from ascites fluid / Source: (natural) Mus musculus (house mouse) / Strain: Balbc / References: UniProt: Q91Z05*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
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 (eV)
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: BL9-2 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 39285 / Num. obs: 39285 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.487 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Lowest resolution: 1.88 Å / % possible obs: 98.8 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 1964 RANDOM
Rwork0.206 --
all0.206 39883 -
obs0.206 39285 -
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 0 246 3611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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