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- PDB-3g5x: Antibodies Specifically Targeting a Locally Misfolded Region of T... -

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Basic information

Entry
Database: PDB / ID: 3g5x
TitleAntibodies Specifically Targeting a Locally Misfolded Region of Tumor Associated EGFR
Components
  • 806 heavy chain
  • 806 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: 2.3 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 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 12, 2011Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 806 light chain
B: 806 heavy chain
C: 806 light chain
D: 806 heavy chain


Theoretical massNumber of molelcules
Total (without water)93,6014
Polymers93,6014
Non-polymers00
Water3,747208
1
A: 806 light chain
B: 806 heavy chain


Theoretical massNumber of molelcules
Total (without water)46,8012
Polymers46,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-26 kcal/mol
Surface area19080 Å2
MethodPISA
2
C: 806 light chain
D: 806 heavy chain


Theoretical massNumber of molelcules
Total (without water)46,8012
Polymers46,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-26 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.372, 74.624, 83.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13B
23D
14B
24D
15B
25D
16B
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 107
2111C1 - 107
1121A108 - 214
2121C108 - 214
1131B1 - 115
2131D1 - 115
1141B116 - 155
2141D116 - 155
1151B164 - 214
2151D164 - 214
1164B156 - 163
2164D156 - 163

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Antibody 806 light chain


Mass: 23565.803 Da / Num. of mol.: 2
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 806 heavy chain


Mass: 23234.896 Da / Num. of mol.: 2
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.: 208 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.6
Details: 0.1M sodium acetate, 6-8% PEG6000, 15-20% isopropanol, pH4.6, 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: 2.2→29.7 Å / Num. obs: 44905 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.267 / % possible all: 91.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.476 / SU ML: 0.23 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.43 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28891 2011 5.1 %RANDOM
Rwork0.22469 ---
obs0.22792 37397 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.271 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2--2.22 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 0 208 6788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0216754
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9319218
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4935854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57724.662266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.441151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0861520
X-RAY DIFFRACTIONr_chiral_restr0.1220.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025100
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.32738
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.54487
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.5508
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.396
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.523
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5092.54365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4193.56976
X-RAY DIFFRACTIONr_scbond_it2.1132.52767
X-RAY DIFFRACTIONr_scangle_it3.2023.52242
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
1A817tight positional0.140.05
2A838tight positional0.150.05
3B908tight positional0.070.05
4B288tight positional0.150.05
5B375tight positional0.110.05
6B50medium positional1.540.5
1A817tight thermal0.140.3
2A838tight thermal0.130.3
3B908tight thermal0.140.3
4B288tight thermal0.10.3
5B375tight thermal0.090.3
6B50medium thermal0.72
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 155 -
Rwork0.284 2661 -
obs--98.36 %
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)
11.1307-1.0182-0.63351.64521.46822.0529-0.0580.10620.0203-0.0012-0.03120.0727-0.09150.06030.08910.0204-0.0295-0.0279-0.04390.0216-0.05124.19823.67750.164
23.18193.25031.79694.05541.41551.96670.0397-0.20680.21220.2143-0.19790.22040.1739-0.15470.1582-0.0892-0.02190.04640.0456-0.1116-0.0528-9.82613.46345.607
32.04930.29691.01081.05210.16762.372-0.04660.05270.1082-0.1164-0.0666-0.0948-0.14830.09520.1133-0.02510.00720.0322-0.00640.0386-0.051826.38617.45429.411
43.4805-0.14080.1471.37811.39583.1138-0.2436-0.22320.40520.0098-0.14280.15420.026-0.34240.3864-0.0924-0.0105-0.03630.0224-0.15670.0378-10.2223.27633.327
51.388-1.09390.52772.4792-0.76811.6209-0.0617-0.03840.02370.1851-0.0711-0.1058-0.1663-0.03130.1329-0.0245-0.0191-0.0041-0.03020.0053-0.082921.94712.91791.99
63.2062.1332-0.2333.445-1.06041.31990.0196-0.23940.06830.1879-0.0696-0.1375-0.1295-0.02170.05-0.17880.0437-0.0487-0.06660.02070.056455.93921.82387.66
72.28230.3975-0.95451.1497-0.61032.256-0.04750.1447-0.0332-0.06480.0293-0.0016-0.0316-0.24270.0182-0.03380.0211-0.0521-0.0132-0.0177-0.082919.80819.31171.388
82.62990.01710.2871.2303-1.31465.7597-0.1805-0.0277-0.2663-0.1013-0.1729-0.17960.30670.42350.3534-0.14160.04380.053-0.0970.0550.057656.50213.07174.66
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2A109 - 214
3X-RAY DIFFRACTION3B1 - 117
4X-RAY DIFFRACTION4B118 - 214
5X-RAY DIFFRACTION5C1 - 108
6X-RAY DIFFRACTION6C109 - 214
7X-RAY DIFFRACTION7D1 - 117
8X-RAY DIFFRACTION8D118 - 214

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