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- PDB-1c5c: DECARBOXYLASE CATALYTIC ANTIBODY 21D8-HAPTEN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1c5c
TitleDECARBOXYLASE CATALYTIC ANTIBODY 21D8-HAPTEN COMPLEX
Components(CHIMERIC DECARBOXYLASE ANTIBODY 21D8) x 2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / CATALYTIC ANTIBODY / CHIMERIC FAB / DECARBOXYLASE / HAPTEN COMPLEX
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 2-ACETYLAMINO-NAPTHALENE-1,5-DISULFONIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsHotta, K. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Catalysis of decarboxylation by a preorganized heterogeneous microenvironment: crystal structures of abzyme 21D8.
Authors: Hotta, K. / Lange, H. / Tantillo, D.J. / Houk, K.N. / Hilvert, D. / Wilson, I.A.
History
DepositionNov 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: CHIMERIC DECARBOXYLASE ANTIBODY 21D8
H: CHIMERIC DECARBOXYLASE ANTIBODY 21D8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0505
Polymers46,5212
Non-polymers5303
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-27 kcal/mol
Surface area20180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)39.217, 43.932, 221.205
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 CHIMERIC DECARBOXYLASE ANTIBODY 21D8


Mass: 23547.086 Da / Num. of mol.: 1 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Details: THE CONSTANT DOMAIN (RESIDUES 103-214) IS FROM HUMAN SOURCE, AND THE VARIABLE DOMAIN (RESIDUES 1-102) IS FROM MURINE SOURCE
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: BALB/C, BALB/C / Cell: B-LYMPHOCYTE / Cell line: 21D8 / Organ: SPLEEN / Plasmid: P4XH-M13 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#2: Antibody CHIMERIC DECARBOXYLASE ANTIBODY 21D8


Mass: 22973.838 Da / Num. of mol.: 1 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Details: THE CONSTANT DOMAIN (RESIDUES 109-230) IS FROM HUMAN SOURCE, AND THE VARIABLE DOMAIN (RESIDUES 1-108) IS FROM MURINE SOURCE
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: BALB/C, BALB/C / Cell: B-LYMPHOCYTE / Cell line: 21D8 / Organ: SPLEEN / Plasmid: P4XH-M13 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#3: Chemical ChemComp-TK4 / 2-ACETYLAMINO-NAPTHALENE-1,5-DISULFONIC ACID


Mass: 345.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO7S2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE NUMBERING ACCORDING TO THE KABAT & WU SCHEME

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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: 37.98 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 22.5 ℃ / pH: 5.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
126 mMprotein1drop
250 mMsodium acetate1drop
321.5 %(w/v)mPEG50001reservoir
4100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 74 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 49213 / % possible obs: 96.6 % / Redundancy: 3.6 % / Rsym value: 0.054 / Net I/σ(I): 20.5
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.38 / Rsym value: 0.421 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 176796 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FRG AND 1GAF

1frg

1gaf


Resolution: 1.61→10 Å / Num. parameters: 14592 / Num. restraintsaints: 13877 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 4790 11.3 %RANDOM
all0.1882 42517 --
obs0.1934 -84.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 3229 / Occupancy sum non hydrogen: 3615
Refinement stepCycle: LAST / Resolution: 1.61→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 34 311 3615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.048
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.072
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.1
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg29.3
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.3

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