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- PDB-1c5b: DECARBOXYLASE CATALYTIC ANTIBODY 21D8 UNLIGANDED FORM -

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Basic information

Entry
Database: PDB / ID: 1c5b
TitleDECARBOXYLASE CATALYTIC ANTIBODY 21D8 UNLIGANDED FORM
Components(CHIMERIC DECARBOXYLASE ANTIBODY 21D8) x 2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / CATALYTIC ANTIBODY / CHIMERIC FAB / DECARBOXYLASE / UNLIGANDED
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 8, 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 / 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 1.4Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)46,5212
Polymers46,5212
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-27 kcal/mol
Surface area19380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)39.258, 43.345, 59.500
Angle α, β, γ (deg.)88.02, 79.10, 89.92
Int Tables number1
Space group name H-MP1

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 297.5 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 21.5% (W/V) MPEG 5000 IN 0.1 M NAOAC AT PH 5.5 MIXED 1:1 WITH 20MG/ML PROTEIN, VAPOR DIFFUSION, SITTING DROP, temperature 297.5K
Crystal grow
*PLUS
Temperature: 22.5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 mg/mlprotein1drop
250 mMsodium acetate1drop
333 %(v/v)mPEG50001reservoir
4100 mMimidazole malate1reservoir
52-acetamido-1,5-naphthalane disulfonate1reservoirtenfold molar excess

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20181 / % possible obs: 89.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.094 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.83 / Rsym value: 0.434 / % possible all: 85.8
Reflection
*PLUS
% possible obs: 91.8 % / Num. measured all: 46419 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 90.8 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
AMoREphasing
CNS0.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FRG AND 1GAF

1frg

1gaf


Resolution: 2.1→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2002 9.9 %RANDOM
Rwork0.188 ---
obs0.188 20181 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.58 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.1 Å23.05 Å21.77 Å2
2--1.82 Å21.7 Å2
3----8.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 0 169 3439
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 316 9.8 %
Rwork0.25 2899 -
obs--85.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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