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- PDB-2dtm: Thermodynamic and structural analyses of hydrolytic mechanism by ... -

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Basic information

Entry
Database: PDB / ID: 2dtm
TitleThermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies
Components(IMMUNOGLOBULIN 6D9) x 2
KeywordsIMMUNE SYSTEM / CATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB / IMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / 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 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
If kappa light chain / Ig heavy chain V region 914
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOda, M. / Ito, N. / Tsumuraya, T. / Suzuki, K. / Fujii, I.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis
Authors: Oda, M. / Ito, N. / Tsumuraya, T. / Suzuki, K. / Sakakura, M. / Fujii, I.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: A structural basis for transition-state stabilization in antibody-catalyzed hydrolysis: crystal structures of an abzyme at 1. 8 A resolution
Authors: Kristensen, O. / Vassylyev, D.G. / Tanaka, F. / Morikawa, K. / Fujii, I.
History
DepositionJul 13, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: IMMUNOGLOBULIN 6D9
H: IMMUNOGLOBULIN 6D9


Theoretical massNumber of molelcules
Total (without water)48,2362
Polymers48,2362
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-25 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.263, 80.762, 89.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IMMUNOGLOBULIN 6D9 / CATALYTIC ANTIBODY 6D9


Mass: 24101.729 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 6D9 MURINE-MURINE HYBRIDOMA / Secretion: ASCITES FLUID / References: UniProt: A2NHM3
#2: Antibody IMMUNOGLOBULIN 6D9 / CATALYTIC ANTIBODY 6D9


Mass: 24134.154 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 6D9 MURINE-MURINE HYBRIDOMA / Secretion: ASCITES FLUID / References: UniProt: P18527
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 50mM Tris-HCl(pH 8.7), 16%(w/v) PEG4000, 0.1mM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Dec 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. all: 22833 / Num. obs: 22833 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.046

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DQT

2dqt


Resolution: 2.25→14.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1335318.12 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2302 10.1 %RANDOM
Rwork0.223 ---
obs0.223 22795 95.3 %-
all-22795 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.2453 Å2 / ksol: 0.3115 e/Å3
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å20 Å20 Å2
2--5.83 Å20 Å2
3----10.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.25→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 0 95 3397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
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
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 363 10 %
Rwork0.365 3276 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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