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- PDB-2gk0: Structure of Catalytic Elimination Antibody 13G5 from a twinned c... -

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Basic information

Entry
Database: PDB / ID: 2gk0
TitleStructure of Catalytic Elimination Antibody 13G5 from a twinned crystal in space group C2
Components
  • Catalytic elimination antibody 13G5 heavy chain
  • Catalytic elimination antibody 13G5 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / catalytic antibody / elimination
Function / homology
Function and homology information


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
Kappa light chain C_region / Ighg protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDebler, E.W. / Wilson, I.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Bifunctional Catalysis of Proton Transfer at an Antibody Active Site.
Authors: Muller, R. / Debler, E.W. / Steinmann, M. / Seebeck, F.P. / Wilson, I.A. / Hilvert, D.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Catalytic elimination antibody 13G5 light chain
H: Catalytic elimination antibody 13G5 heavy chain
A: Catalytic elimination antibody 13G5 light chain
B: Catalytic elimination antibody 13G5 heavy chain


Theoretical massNumber of molelcules
Total (without water)94,8424
Polymers94,8424
Non-polymers00
Water1,27971
1
L: Catalytic elimination antibody 13G5 light chain
H: Catalytic elimination antibody 13G5 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,4212
Polymers47,4212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-23 kcal/mol
Surface area19500 Å2
MethodPISA
2
A: Catalytic elimination antibody 13G5 light chain
B: Catalytic elimination antibody 13G5 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,4212
Polymers47,4212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-24 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.875, 84.619, 150.074
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-237-

HOH

DetailsThis entry contains the crystallographic asymmetric unit which consists of 2 biological molecules: LH, and AB

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Components

#1: Antibody Catalytic elimination antibody 13G5 light chain


Mass: 23939.566 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q65ZC0
#2: Antibody Catalytic elimination antibody 13G5 heavy chain


Mass: 23481.295 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91Z05
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: PEG 4000, 0.3M NaHCOO, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 31459 / Num. obs: 30830 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 49.2 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.4
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.58 / % possible all: 92.9

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Processing

Software
NameClassification
ADSCdata collection
DENZOdata reduction
AMoREphasing
SHELXL-97refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GJZ

2gjz


Resolution: 2.45→10 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
Details: The crystal was twinned. The twin fraction is 0.49809. The twin operator is 1 0 0 0 -1 0 0 0 -1.
RfactorNum. reflectionSelection details
Rfree0.2548 1188 RANDOM
Rwork0.1912 --
all0.2357 22676 -
obs0.2357 22222 -
Refinement stepCycle: LAST / Resolution: 2.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6621 0 0 71 6692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d1.6
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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