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- PDB-3gnm: The crystal structure of the JAA-F11 monoclonal antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 3gnm
TitleThe crystal structure of the JAA-F11 monoclonal antibody Fab fragment
Components
  • JAA-F11 Fab Antibody Fragment, Heavy Chain
  • JAA-F11 Fab Antibody Fragment, Light Chain
KeywordsIMMUNE SYSTEM / Antibody / immunoglobulin / JAA-F11 / Thompson-Friedenreich antigen
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGulick, A.M. / Rittenhouse-Olson, K. / Jadey, S.
CitationJournal: Plos One / Year: 2013
Title: Computational Screening of the Human TF-Glycome Provides a Structural Definition for the Specificity of Anti-Tumor Antibody JAA-F11.
Authors: Tessier, M.B. / Grant, O.C. / Heimburg-Molinaro, J. / Smith, D. / Jadey, S. / Gulick, A.M. / Glushka, J. / Deutscher, S.L. / Rittenhouse-Olson, K. / Woods, R.J.
History
DepositionMar 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 13, 2013Group: Database references
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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: JAA-F11 Fab Antibody Fragment, Light Chain
H: JAA-F11 Fab Antibody Fragment, Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7784
Polymers48,4782
Non-polymers3002
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-21 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.210, 94.210, 94.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody JAA-F11 Fab Antibody Fragment, Light Chain


Mass: 24232.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#2: Antibody JAA-F11 Fab Antibody Fragment, Heavy Chain


Mass: 24245.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 26% PEG 5000, 50 mM LiBr, 50 mM NaCitrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2007
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 25405 / Num. obs: 25154 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3170 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CHESSOperating Softwaredata collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CLZ

1clz


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.886 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26255 1225 4.8 %RANDOM
Rwork0.18521 ---
obs0.18878 24063 99.04 %-
all-24296 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 20 176 3529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223451
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9514700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3645437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58824.148135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22715536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9861512
X-RAY DIFFRACTIONr_chiral_restr0.1430.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212597
X-RAY DIFFRACTIONr_mcbond_it1.0821.52171
X-RAY DIFFRACTIONr_mcangle_it1.8623522
X-RAY DIFFRACTIONr_scbond_it3.10831280
X-RAY DIFFRACTIONr_scangle_it4.6444.51176
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 95 -
Rwork0.199 1685 -
obs--96.74 %
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)
11.8050.6937-0.61912.4178-1.32492.84720.0458-0.03130.08760.0154-0.0168-0.033-0.298-0.1565-0.0290.05080.0298-0.00170.1146-0.01410.0141-14.135-11.791-29.905
22.7168-0.96440.62021.0338-0.20891.2204-0.0607-0.05620.02820.03990.0155-0.14060.01050.07720.04520.055-0.00730.00470.08070.00160.0544-8.835-25.332-1.513
32.0706-1.35831.61011.6414-1.26113.25490.07370.18640.0207-0.0512-0.1677-0.061-0.14330.29990.09390.0341-0.0348-0.00160.13580.02520.02473.93-22.822-34.397
42.6069-1.0226-0.77640.9780.53550.7565-0.0855-0.0693-0.32750.1273-0.0140.18230.17190.08380.09950.08380.00920.02030.05780.04020.0919-7.842-41.115-2.414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 118
2X-RAY DIFFRACTION2H121 - 218
3X-RAY DIFFRACTION3L1 - 111
4X-RAY DIFFRACTION4L115 - 217

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