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- PDB-3l1o: Crystal structure of monoclonal antibody MN423 Fab fragment with ... -

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Basic information

Entry
Database: PDB / ID: 3l1o
TitleCrystal structure of monoclonal antibody MN423 Fab fragment with free combining site, crystallized in the presence of zinc
Components(MONOCLONAL ANTIBODY FAB FRAGMENT MN423 ...) x 2
KeywordsIMMUNE SYSTEM / monoclonal antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IMIDAZOLE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSkrabana, R. / Sevcik, J.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Monoclonal antibody MN423 as a stable mold facilitates structure determination of disordered tau protein
Authors: Skrabana, R. / Dvorsky, R. / Sevcik, J. / Novak, M.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
H: MONOCLONAL ANTIBODY FAB FRAGMENT MN423 H CHAIN
L: MONOCLONAL ANTIBODY FAB FRAGMENT MN423 L CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9126
Polymers47,7312
Non-polymers1804
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-27 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.330, 75.426, 72.701
Angle α, β, γ (deg.)90.00, 92.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody MONOCLONAL ANTIBODY FAB FRAGMENT MN423 H CHAIN


Mass: 23951.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody MONOCLONAL ANTIBODY FAB FRAGMENT MN423 L CHAIN


Mass: 23779.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 4 types, 438 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 3350, 0.1M IMIDAZOLE, 0.01M ZNSO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8166 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2006
RadiationMonochromator: Ge(111) triangular bent crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8166 Å / Relative weight: 1
ReflectionResolution: 2→19.9 Å / Num. all: 24684 / Num. obs: 24684 / % possible obs: 84.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.065
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 5 / Num. unique all: 2203 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V17

2v17


Resolution: 2→19.9 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.334 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1253 5.1 %RANDOM
Rwork0.15789 ---
all0.16237 24684 --
obs0.16237 23431 81.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å2-0.17 Å2
2---1.94 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 8 434 3772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223444
X-RAY DIFFRACTIONr_bond_other_d0.0010.022316
X-RAY DIFFRACTIONr_angle_refined_deg2.1921.9564694
X-RAY DIFFRACTIONr_angle_other_deg1.1093.0045643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6995443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76623.806134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3515547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9161517
X-RAY DIFFRACTIONr_chiral_restr0.1350.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02697
X-RAY DIFFRACTIONr_nbd_refined0.2070.2570
X-RAY DIFFRACTIONr_nbd_other0.2120.22373
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21576
X-RAY DIFFRACTIONr_nbtor_other0.0990.21868
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2327
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.225
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined00.21
X-RAY DIFFRACTIONr_mcbond_it1.1821.52191
X-RAY DIFFRACTIONr_mcbond_other0.3871.5886
X-RAY DIFFRACTIONr_mcangle_it1.92923545
X-RAY DIFFRACTIONr_scbond_it3.18231309
X-RAY DIFFRACTIONr_scangle_it4.6584.51145
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 112 -
Rwork0.168 2091 -
obs--99.68 %
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)
11.3387-0.0082-0.12581.1743-0.0870.8022-0.01860.01910.1031-0.0344-0.03390.0379-0.04170.02270.0525-0.0255-0.0035-0.01480.0496-0.00260.0954-0.42411.516-4.012
23.0791-2.04741.38213.3751-1.56893.9315-0.024-0.0888-0.41180.28170.17770.0624-0.2225-0.0192-0.1537-0.00220.00940.00990.05780.00440.03531.9163.92128.61
37.0433-6.02230.3765.154-0.48926.0344-0.15730.17770.2879-0.3010.1345-0.42580.06150.44560.02270.00150.02130.02170.07650.03150.05557.9851.54223.314
41.0281-0.03350.35772.5845-0.34922.7722-0.0398-0.1953-0.03980.40410.0642-0.1268-0.22020.1195-0.02450.02160.0154-0.00910.0363-0.00920.02715.4345.92633.726
55.7947-1.80673.021.3924-0.9782.89840.158-0.0292-0.0935-0.0675-0.0410.04370.1275-0.1985-0.117-0.00150.0214-0.00320.0478-0.02830.093712.108-12.41-2.336
62.2428-0.460.47273.16970.89692.873-0.05280.23690.1846-0.0449-0.102-0.08930.07030.28210.1548-0.0231-0.00750.00090.080.02610.074212.064-1.534-8.22
70.8744-0.2226-0.37440.5477-0.271.39550.0144-0.0325-0.00550.0086-0.049-0.03840.06870.15550.0346-0.0246-0.0176-0.00970.032-0.01030.111411.527-6.3288.451
83.37490.416-3.13371.0004-0.44454.92030.03950.0511-0.0040.17010.00410.05330.1137-0.0744-0.04360.02-0.0293-0.02670.0734-0.01360.04352.872-13.63729.669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 123
2X-RAY DIFFRACTION2H124 - 164
3X-RAY DIFFRACTION3H165 - 180
4X-RAY DIFFRACTION4H181 - 227
5X-RAY DIFFRACTION5L1 - 24
6X-RAY DIFFRACTION6L25 - 54
7X-RAY DIFFRACTION7L55 - 141
8X-RAY DIFFRACTION8L142 - 214

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