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- PDB-3fo9: Crystal structure of aldolase antibody 33F12 Fab' in complex with... -

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Basic information

Entry
Database: PDB / ID: 3fo9
TitleCrystal structure of aldolase antibody 33F12 Fab' in complex with hapten 1,3-diketone
Components
  • Immunoglobulin IGG2A - heavy chain
  • Immunoglobulin IGG2A - light chain
KeywordsIMMUNE SYSTEM / aldolase antibody / enamine intermediate / amine catalysis
Function / homology
Function and homology information


positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment ...positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / multivesicular body / response to bacterium / positive regulation of immune response / antibacterial humoral response / extracellular space / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-DIK / Ig gamma-2A chain C region, membrane-bound form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Direct observation of an enamine intermediate in amine catalysis
Authors: Zhu, X. / Tanaka, F. / Lerner, R.A. / Barbas, C.F. / Wilson, I.A.
History
DepositionDec 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: Immunoglobulin IGG2A - light chain
H: Immunoglobulin IGG2A - heavy chain
A: Immunoglobulin IGG2A - light chain
B: Immunoglobulin IGG2A - heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5806
Polymers95,9454
Non-polymers6352
Water4,288238
1
L: Immunoglobulin IGG2A - light chain
H: Immunoglobulin IGG2A - heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2903
Polymers47,9732
Non-polymers3171
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-26 kcal/mol
Surface area19850 Å2
MethodPISA
2
A: Immunoglobulin IGG2A - light chain
B: Immunoglobulin IGG2A - heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2903
Polymers47,9732
Non-polymers3171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-27 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.830, 81.038, 174.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Immunoglobulin IGG2A - light chain


Mass: 24142.783 Da / Num. of mol.: 2 / Fragment: light chain of 33F12 Fab' fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: MUS MUSCULUS (house mouse)
#2: Antibody Immunoglobulin IGG2A - heavy chain


Mass: 23829.885 Da / Num. of mol.: 2 / Fragment: heavy chain of 33F12 Fab' fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: MUS MUSCULUS (house mouse) / References: UniProt: P01865*PLUS
#3: Chemical ChemComp-DIK / 5-{[4-(5-methyl-3-oxohex-4-en-1-yl)phenyl]amino}-5-oxopentanoic acid


Mass: 317.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7.4
Details: 30% PEG 4000, 10% isopropanol, 0.1M Hepes., pH 7.4, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2005
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.56 Å / Num. obs: 71502 / % possible obs: 96.1 % / Rmerge(I) obs: 0.054 / Χ2: 1.933 / Net I/σ(I): 36.891
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.940.48634700.847171.1
1.94-1.990.39240680.883183.1
1.99-2.050.34245970.947194
2.05-2.110.2848151.072198.6
2.11-2.170.21548831.183199.5
2.17-2.250.19449101.272199.9
2.25-2.340.15749091.362199.9
2.34-2.450.12949361.4511100
2.45-2.580.10649061.6241100
2.58-2.740.08649681.85199.8
2.74-2.950.06849142.201199.8
2.95-3.250.05849822.699199.6
3.25-3.720.0549863.12199.6
3.72-4.680.04349943.19198.7
4.68-500.0451643.025197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AXT

1axt


Resolution: 1.9→43.56 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.219 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU B: 8.556 / SU ML: 0.121 / SU R Cruickshank DPI: 0.177 / SU Rfree: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3601 5 %RANDOM
Rwork0.215 ---
obs0.216 71432 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.77 Å2 / Biso mean: 41.536 Å2 / Biso min: 24.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20 Å2
2---0.25 Å20 Å2
3---1.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 44 238 7028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226962
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.969464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95723.897272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.532151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6141530
X-RAY DIFFRACTIONr_chiral_restr0.090.21054
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025230
X-RAY DIFFRACTIONr_nbd_refined0.20.22813
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24698
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2341
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.217
X-RAY DIFFRACTIONr_mcbond_it0.7821.54460
X-RAY DIFFRACTIONr_mcangle_it1.27527058
X-RAY DIFFRACTIONr_scbond_it1.74632919
X-RAY DIFFRACTIONr_scangle_it2.6244.52406
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 205 -
Rwork0.289 3653 -
all-3858 -
obs--71.91 %
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)
11.24980.326-0.82890.7714-0.18150.8-0.180.13230.0211-0.08670.13340.0140.0587-0.150.0466-0.0233-0.08210.02020.01940.0195-0.04973.776718.850579.257
21.65710.6815-0.01431.04160.55791.2058-0.0267-0.0373-0.0190.0340.0103-0.13430.1890.08950.0164-0.02740.0261-0.0038-0.04140.0117-0.014338.860526.513266.9434
32.650.6982-0.35361.07150.25321.2533-0.0675-0.06690.31430.03240.06180.2469-0.0404-0.1030.0057-0.05950.0252-0.0099-0.03790.01440.01284.515338.70387.8351
40.7853-0.1238-0.41610.76350.1911.65930.05090.02360.1203-0.11080.0148-0.09640.0244-0.0094-0.0657-0.00510.0215-0.0046-0.04140.0164-0.022130.027739.787666.7755
51.46840.40910.20010.86990.14081.4887-0.1149-0.03210.10540.08550.08810.07590.0713-0.18390.0269-0.06120.02340.0296-0.05460.04160.01757.580255.251466.5855
61.9442-0.3774-0.88920.71640.72981.33590.01610.0044-0.17180.0794-0.04970.06360.1425-0.0250.0335-0.0507-0.0138-0.0027-0.05520.03850.016411.960231.806937.0893
70.7273-0.0376-0.27290.80760.57691.196-0.06950.07460.1960.00880.06510.0595-0.10180.02820.0044-0.04850.0128-0.025-0.06920.07230.0622.676267.25256.7037
81.30710.66360.44120.72980.66140.9376-0.0170.0249-0.012-0.04910.00820.0724-0.0654-0.01110.0089-0.0626-0.0199-0.0076-0.0390.06150.026113.934147.039132.3638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 105
2X-RAY DIFFRACTION2L106 - 214
3X-RAY DIFFRACTION3H1 - 105
4X-RAY DIFFRACTION4H106 - 228
5X-RAY DIFFRACTION5A1 - 105
6X-RAY DIFFRACTION6A106 - 214
7X-RAY DIFFRACTION7B1 - 105
8X-RAY DIFFRACTION8B106 - 228

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