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- PDB-2dqu: Crystal form II: high resolution crystal structure of the complex... -

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Basic information

Entry
Database: PDB / ID: 2dqu
TitleCrystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog
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 / extracellular region / metal ion binding
Similarity search - Function
: / : / 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
Chem-CPD / If kappa light chain / Ig heavy chain V region 914
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKristensen, O. / Vassylyev, D.G. / Tanaka, F. / Ito, N. / Morikawa, 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: 1997
Title: Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme: evidence for an essential histidine involved in transition state stabilization
Authors: Miyashita, H. / Hara, T. / Tanimura, R. / Fukuyama, S. / Cagnon, C. / Kohara, A. / Fujii, I.
#2: Journal: J.Am.Chem.Soc. / Year: 1995
Title: Correlation between Antigen-Combining-Site Structures and Functions within a Panel of Catalytic Antibodies Generated against a Single Transition State Analog
Authors: Fujii, I. / Tanaka, F. / Miyashita, H. / Tanimura, R. / Kinoshita, K.
#3: Journal: Protein Pept.Lett. / Year: 1995
Title: Crystallization and Preliminary X-Ray Analysis: Transition State Complex of a Chloramphenicol Prodrug Activation Specific Catalytic Antibody
Authors: Kristensen, O. / Miyashita, H. / Vassylyev, D.G. / Tanaka, F. / Fujii, I. / Morikawa, K.
#4: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1994
Title: A common ancestry for multiple catalytic antibodies generated against a single transition-state analog
Authors: Miyashita, H. / Hara, T. / Tanimura, R. / Tanaka, F. / Kikuchi, M. / Fujii, I.
#5: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1994
Title: A common ancestry for multiple catalytic antibodies generated against a single transition-state analog
Authors: Miyashita, H. / Hara, T. / Tamimura, R. / Tanaka, F. / Kikuchi, M. / Fujii, I.
#6: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1993
Title: Prodrug activation via catalytic antibodies
Authors: Miyashita, H. / Karaki, Y. / Kikuchi, M. / Fujii, I.
#7: Journal: To be Published
Title: Thermodynamic and Structural Analyses of Hydrolytic Mechanism by Catalytic Antibodies
Authors: Oda, M. / Ito, N. / Tsumuraya, T. / Suzuki, K. / Fujii, I.
History
DepositionMay 30, 2006Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 20, 2006ID: 1HYY
Revision 1.0Jun 20, 2006Provider: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,9793
Polymers48,2362
Non-polymers7431
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-33 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.700, 63.040, 56.560
Angle α, β, γ (deg.)90.00, 98.75, 90.00
Int Tables number4
Space group name H-MP1211

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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*PLUS
#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*PLUS
#3: Chemical ChemComp-CPD / [1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER


Mass: 743.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H36Cl2F3N6O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.05 Å3/Da / Density % sol: 40 %
Description: DATA WAS COLLECTED USING THE WEISSENBERG METHOD.
Crystal growpH: 8.3
Details: THE PRE-FORMED COMPLEX WAS CRYSTALLIZED FROM 17% PEG 4000, 50MM TRIS, 0.1MM EDTA, PH 8.3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 15, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 38032 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.082

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS1.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DQT

2dqt


Resolution: 1.7→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 14979897.84 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1898 5 %RANDOM
Rwork0.207 ---
obs0.207 38028 84.4 %-
all-38028 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.3596 Å2 / ksol: 0.320648 e/Å3
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1--4.01 Å20 Å2-2.35 Å2
2--4.5 Å20 Å2
3----0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 48 257 3679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
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: 1.7→1.81 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 216 5.1 %
Rwork0.336 4028 -
obs--56.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3cpd.parcpd.top

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