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- PDB-1c1e: CRYSTAL STRUCTURE OF A DIELS-ALDERASE CATALYTIC ANTIBODY 1E9 IN C... -

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Basic information

Entry
Database: PDB / ID: 1c1e
TitleCRYSTAL STRUCTURE OF A DIELS-ALDERASE CATALYTIC ANTIBODY 1E9 IN COMPLEX WITH ITS HAPTEN
Components
  • CATALYTIC ANTIBODY 1E9 (HEAVY CHAIN)
  • CATALYTIC ANTIBODY 1E9 (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / CATALYTIC ANTIBODY / DIELS-ALDER / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-ENH / D-MALATE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsXu, J. / Wilson, I.A.
CitationJournal: Science / Year: 1999
Title: Evolution of shape complementarity and catalytic efficiency from a primordial antibody template.
Authors: Xu, J. / Deng, Q. / Chen, J. / Houk, K.N. / Bartek, J. / Hilvert, D. / Wilson, I.A.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2013Group: Non-polymer description
Revision 1.4Oct 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: CATALYTIC ANTIBODY 1E9 (LIGHT CHAIN)
H: CATALYTIC ANTIBODY 1E9 (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0084
Polymers47,4902
Non-polymers5182
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-62 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.73, 132.44, 167.50
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-765-

HOH

21L-783-

HOH

31L-806-

HOH

41H-704-

HOH

51H-764-

HOH

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Components

#1: Antibody CATALYTIC ANTIBODY 1E9 (LIGHT CHAIN)


Mass: 23865.527 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody CATALYTIC ANTIBODY 1E9 (HEAVY CHAIN)


Mass: 23624.840 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-ENH / 1,7,8,9,10,10-HEXACHLORO-4-METHYL-4-AZA-TRICYCLO[5.2.1.0(2,6)]DEC-8-ENE-3,5-DIONE


Mass: 383.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H5Cl6NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 10K, IMIDAZOLIUM MALATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal grow
*PLUS
Method: unknown
Details: hapten and 1E9 Fab fragment were mixed in a 10:1 molar ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 mg/ml1E9 Fab11
214 %PEG1000012
3100 mMimidazolium malate12

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Data collection

DiffractionMean temperature: 97.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→19.96 Å / Num. all: 39810 / Num. obs: 39213 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 15.17 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 1.2 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 126249
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR98refinement
RefinementResolution: 1.9→20 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD TARGET USED
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1521 -5% RANDOM
Rwork0.239 ---
all0.256 30764 --
obs0.25 30764 86.2 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 28 195 3563
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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