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- PDB-3g5z: Antibodies Specifically Targeting a Locally Misfolded Region of T... -

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Basic information

Entry
Database: PDB / ID: 3g5z
TitleAntibodies Specifically Targeting a Locally Misfolded Region of Tumor Associated EGFR
Components
  • 175 heavy chain
  • 175 light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGarrett, T.P.J. / Burgess, A.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Antibodies specifically targeting a locally misfolded region of tumor associated EGFR
Authors: Garrett, T.P.J. / Burgess, A.W. / Gan, H.K. / Luwor, R.B. / Cartwright, G. / Walker, F. / Orchard, S.G. / Clayton, A.H.A. / Nice, E.C. / Rothacker, J. / Catimel, B. / Cavenee, W.K. / Old, L. ...Authors: Garrett, T.P.J. / Burgess, A.W. / Gan, H.K. / Luwor, R.B. / Cartwright, G. / Walker, F. / Orchard, S.G. / Clayton, A.H.A. / Nice, E.C. / Rothacker, J. / Catimel, B. / Cavenee, W.K. / Old, L.J. / Stockert, E. / Ritter, G. / Adams, T.E. / Hoyne, P.A. / Wittrup, D. / Chao, G. / Cochran, J.R. / Luo, C. / Lou, M. / Huyton, T. / Xu, Y. / Fairlie, W.D. / Yao, S. / Scott, A.M. / Johns, T.G.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 12, 2011Group: Structure summary
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: 175 light chain
B: 175 heavy chain


Theoretical massNumber of molelcules
Total (without water)46,5772
Polymers46,5772
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-26 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.370, 94.800, 108.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 175 light chain


Mass: 23229.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA CELL / Production host: Mus musculus (house mouse)
#2: Antibody 175 heavy chain


Mass: 23347.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA CELL / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 9
Details: 0.2M NH4 acetate, 24% PEG6K, 0.1M Bis-tris propane, pH9.0, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9171 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.14
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.332 / % possible all: 90.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→35.75 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.825 / SU B: 32.739 / SU ML: 0.332 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30121 534 4.8 %RANDOM
Rwork0.2138 ---
obs0.2179 9171 92.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.986 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---1 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 0 39 3315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223364
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9454597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.56424.47132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.10415514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6891511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022555
X-RAY DIFFRACTIONr_nbd_refined0.2460.21630
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2163
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.211
X-RAY DIFFRACTIONr_mcbond_it1.42732176
X-RAY DIFFRACTIONr_mcangle_it2.59753488
X-RAY DIFFRACTIONr_scbond_it3.67771373
X-RAY DIFFRACTIONr_scangle_it5.306101109
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 24 -
Rwork0.318 486 -
obs--59.1 %
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)
10.2638-0.2911-0.09360.4220.35580.8805-0.01890.02480.01270.04290.037-0.0152-0.0627-0.0028-0.01820.0258-0.0204-0.00460.0035-0.00630.029340.391673.851940.6357
20.1755-0.03940.02271.35450.49250.4665-0.0142-0.0119-0.06150.09250.0444-0.0621-0.0067-0.0225-0.03030.02530.00530.01970.02140.01150.004225.880640.641753.3726
30.05960.193-0.10260.6642-0.51351.0161-0.0052-0.00110.0096-0.0297-0.0212-0.00480.0704-0.02960.02630.01960.00940.0010.00770.01050.039835.931865.164121.4559
41.37360.1857-1.12631.70230.18630.9919-0.01180.06280.1206-0.04560.0470.18340.0025-0.0207-0.0351-0.00540.0168-0.0144-0.01170.0260.050816.78447.38842.1465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 106
2X-RAY DIFFRACTION2A110 - 213
3X-RAY DIFFRACTION3B1 - 114
4X-RAY DIFFRACTION4B120 - 217

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