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- PDB-3fo0: Crystal structure of hapten complex of catalytic elimination anti... -

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Basic information

Entry
Database: PDB / ID: 3fo0
TitleCrystal structure of hapten complex of catalytic elimination antibody 13G5 (wild-type)
Components
  • Catalytic antibody Fab 13G5 IgG2b heavy chain chimera
  • Catalytic antibody Fab 13G5 kappa light chain chimera
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / CATALYTIC ANTIBODY / CHIMERIC FAB / HAPTEN COMPLEX / ACID BASE CATALYSIS / PROTON TRANSFER / Immunoglobulin domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-BZH
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDebler, E.W. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket.
Authors: Debler, E.W. / Muller, R. / Hilvert, D. / Wilson, I.A.
History
DepositionDec 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Catalytic antibody Fab 13G5 kappa light chain chimera
H: Catalytic antibody Fab 13G5 IgG2b heavy chain chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6534
Polymers48,2992
Non-polymers3542
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-23.6 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.071, 87.001, 59.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody Catalytic antibody Fab 13G5 kappa light chain chimera


Mass: 24002.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The variable domain (residues 1-107) is from murine source and the constant domain (residues 108-214) is from human source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#2: Antibody Catalytic antibody Fab 13G5 IgG2b heavy chain chimera


Mass: 24296.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The variable domain (residues 1-113) is from murine source and the constant domain (residues 114-235) is from human source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#3: Chemical ChemComp-BZH / 5-[(2-AMINO-1H-BENZIMIDAZOL-6-YL)AMINO]-5-OXOPENTANOIC ACID


Mass: 262.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCES OF THE FAB COMPLEXES ARE NOT AVAILABLE IN ANY SEQUENCE DATABASES.

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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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2006 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15696 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.076 / Net I/σ(I): 36.3
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.552 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GJZ

2gjz


Resolution: 2.5→32.39 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 25.291 / SU ML: 0.265 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.856 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27684 800 5.1 %RANDOM
Rwork0.2187 ---
obs0.22163 14790 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.185 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å20 Å20 Å2
2---4.93 Å20 Å2
3---2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 25 49 3343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223378
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9624601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78624.766128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00415534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.128159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022535
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21287
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22195
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2152
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5971.52190
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75423466
X-RAY DIFFRACTIONr_scbond_it1.36431388
X-RAY DIFFRACTIONr_scangle_it2.0394.51135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 61 -
Rwork0.338 1061 -
obs--98.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.38561.9969-0.35345.7093-1.29172.6074-0.0230.2567-0.1248-0.4151-0.02060.0370.2236-0.18960.0437-0.17730.0406-0.0053-0.0998-0.0424-0.023911.8058-9.1594-38.3325
22.23390.4644-1.64033.05980.43789.62730.3959-0.2524-0.10160.8945-0.12550.287-0.3835-0.8926-0.27040.0148-0.08120.0327-0.00270.0690.0951-3.4809-28.2564-9.3827
32.5494-0.1687-2.02442.23680.35233.75950.0090.00090.09730.2747-0.0423-0.2658-0.1119-0.01850.0333-0.192-0.0206-0.0793-0.16840.04410.051419.40132.5717-21.9344
42.6533-4.0583-1.48079.75222.07712.6618-0.0859-0.2531-0.12490.93680.0798-0.43870.11480.25550.00610.1273-0.0812-0.0988-0.03610.0027-0.08311.5195-21.6428-5.177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION2L108 - 211
3X-RAY DIFFRACTION3H1 - 113
4X-RAY DIFFRACTION4H114 - 227

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