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- PDB-3fo2: Crystal structure of hapten complex of catalytic elimination anti... -

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Basic information

Entry
Database: PDB / ID: 3fo2
TitleCrystal structure of hapten complex of catalytic elimination antibody 13G5 (Glu(L39)Gln mutant)
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: 2.18 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 / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 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: Catalytic antibody Fab 13G5 kappa light chain chimera
H: Catalytic antibody Fab 13G5 IgG2b heavy chain chimera
A: Catalytic antibody Fab 13G5 kappa light chain chimera
B: Catalytic antibody Fab 13G5 IgG2b heavy chain chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1216
Polymers96,5964
Non-polymers5252
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-25.8 kcal/mol
Surface area19400 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-25.4 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.116, 86.220, 113.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12L
22A
13H
23B
14H
24B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116L1 - 107
2116A1 - 107
1126L108 - 211
2126A108 - 211
1136H1 - 113
2136B1 - 113
1146H114 - 227
2146B114 - 227

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 24001.811 Da / Num. of mol.: 2 / Mutation: E39Q
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.: 2
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.: 2 / Source method: obtained synthetically / Formula: C12H14N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.11 Å3/Da / Density % sol: 41.62 %
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: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 39309 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.093 / Net I/σ(I): 15.9
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.613 / % possible all: 87.8

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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: 2.18→31.27 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.166 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25583 1994 5 %RANDOM
Rwork0.2014 ---
obs0.20404 37589 91.89 %-
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: 43.444 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2--0.14 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.18→31.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6538 0 38 162 6738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226746
X-RAY DIFFRACTIONr_bond_other_d0.0080.024472
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9619192
X-RAY DIFFRACTIONr_angle_other_deg0.8673.00410948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32424.766256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.063151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3371518
X-RAY DIFFRACTIONr_chiral_restr0.0850.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021282
X-RAY DIFFRACTIONr_nbd_refined0.1920.21063
X-RAY DIFFRACTIONr_nbd_other0.2040.24314
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23153
X-RAY DIFFRACTIONr_nbtor_other0.0920.23779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4611.55381
X-RAY DIFFRACTIONr_mcbond_other0.1571.51736
X-RAY DIFFRACTIONr_mcangle_it1.24926932
X-RAY DIFFRACTIONr_scbond_it2.69432971
X-RAY DIFFRACTIONr_scangle_it3.4864.52260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1469loose positional0.245
2A1359loose positional0.355
3A1538loose positional0.185
4A1128loose positional0.235
1H1469loose thermal110
2B1359loose thermal1.0510
3H1538loose thermal0.8210
4B1128loose thermal0.9310
LS refinement shellResolution: 2.18→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 127 -
Rwork0.26 2392 -
obs--80.58 %
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)
11.4933-0.7076-0.07983.39841.00711.76250.0119-0.0569-0.03360.0765-0.09680.0320.03540.03090.0849-0.28920.00210.0056-0.19950.0047-0.2313-32.2295-7.507437.0396
22.1187-0.632-0.18542.2174-0.51698.160.20540.3054-0.0327-0.4174-0.0681-0.20580.07720.753-0.1374-0.20840.03520.0174-0.1645-0.0249-0.1585-17.1385-26.60428.1054
32.4849-0.4828-2.05631.2986-0.12853.86560.00680.00530.1376-0.18510.03060.1136-0.05050.0797-0.0373-0.2384-0.0096-0.0341-0.2819-0.0219-0.2137-39.76254.536420.7608
42.69631.0244-1.22857.3183-1.25032.3017-0.04680.0515-0.3195-0.33830.04630.52480.1621-0.12590.0005-0.13230.036-0.0797-0.147-0.042-0.1736-31.8509-19.5783.8921
52.0781-0.8691-0.72743.505-0.11352.67920.120.04880.1475-0.042-0.1204-0.0764-0.2622-0.1950.0004-0.23140.00230.0033-0.2175-0.0137-0.236-9.140111.350337.0343
61.7755-0.1238-0.68351.79320.59228.78970.03310.28140.1458-0.2802-0.01110.20330.0387-0.6221-0.022-0.19420.0037-0.0149-0.12740.0438-0.1045-24.022829.75687.6378
72.148-0.2641.82611.33730.2883.7719-0.00070.081-0.0647-0.12910.0071-0.1550.0723-0.075-0.0063-0.2158-0.02130.0589-0.25130.017-0.2163-1.4248-0.846720.9329
82.55331.90870.86078.11620.7051.3282-0.0342-0.06910.257-0.2635-0.067-0.492-0.00870.1680.1012-0.120.0260.0616-0.1120.0564-0.1822-9.020723.19543.8464
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 - 221
5X-RAY DIFFRACTION5A1 - 107
6X-RAY DIFFRACTION6A108 - 211
7X-RAY DIFFRACTION7B1 - 113
8X-RAY DIFFRACTION8B114 - 221

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