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- PDB-3p0v: anti-EGFR/HER3 Fab DL11 alone -

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Basic information

Entry
Database: PDB / ID: 3p0v
Titleanti-EGFR/HER3 Fab DL11 alone
Components
  • Fab DL11 heavy chain
  • Fab DL11 light chain
KeywordsIMMUNE SYSTEM / beta-sandwich / antigens EGFR and HER3
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsEigenbrot, C. / Shia, S.
CitationJournal: Cancer Cell / Year: 2011
Title: A two-in-one antibody against HER3 and EGFR has superior inhibitory activity compared with monospecific antibodies.
Authors: Schaefer, G. / Haber, L. / Crocker, L.M. / Shia, S. / Shao, L. / Dowbenko, D. / Totpal, K. / Wong, A. / Lee, C.V. / Stawicki, S. / Clark, R. / Fields, C. / Lewis Phillips, G.D. / Prell, R.A. ...Authors: Schaefer, G. / Haber, L. / Crocker, L.M. / Shia, S. / Shao, L. / Dowbenko, D. / Totpal, K. / Wong, A. / Lee, C.V. / Stawicki, S. / Clark, R. / Fields, C. / Lewis Phillips, G.D. / Prell, R.A. / Danilenko, D.M. / Franke, Y. / Stephan, J.P. / Hwang, J. / Wu, Y. / Bostrom, J. / Sliwkowski, M.X. / Fuh, G. / Eigenbrot, C.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab DL11 light chain
H: Fab DL11 heavy chain
M: Fab DL11 light chain
I: Fab DL11 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9348
Polymers94,7734
Non-polymers1604
Water19811
1
L: Fab DL11 light chain
H: Fab DL11 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4674
Polymers47,3872
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-42 kcal/mol
Surface area19350 Å2
MethodPISA
2
M: Fab DL11 light chain
I: Fab DL11 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4674
Polymers47,3872
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-43 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.375, 77.168, 82.664
Angle α, β, γ (deg.)90.00, 99.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21M
12H
22I

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112L1 - 230
2112M1 - 230
1122H1 - 134
2122I1 - 134
1222H142 - 230
2222I142 - 230

NCS ensembles :
ID
1
2

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Components

#1: Antibody Fab DL11 light chain


Mass: 23385.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pW0579-3 / Production host: Escherichia coli (E. coli)
#2: Antibody Fab DL11 heavy chain


Mass: 24000.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pW0579-3 / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 48.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MgCl/PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 30, 2008
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 20713 / Num. obs: 20173 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.7 % / Biso Wilson estimate: 55 Å2 / Rsym value: 0.135 / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.868 / SU B: 44.118 / SU ML: 0.387 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28018 1064 5.1 %RANDOM
Rwork0.22706 ---
all0.23 20687 --
obs0.22969 19623 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.986 Å2
Baniso -1Baniso -2Baniso -3
1--2.76 Å20 Å2-0.26 Å2
2--4.22 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6493 0 4 11 6508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226667
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9549077
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1545859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1924.615260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.919151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.5361524
X-RAY DIFFRACTIONr_chiral_restr0.0820.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025030
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22517
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24433
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0230.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1932.54356
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.55156922
X-RAY DIFFRACTIONr_scbond_it2.522.52623
X-RAY DIFFRACTIONr_scangle_it3.74852155
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
1L852tight positional0.040.05
2H860tight positional0.040.05
1L785medium positional0.270.5
2H736medium positional0.160.5
1L852tight thermal0.080.5
2H860tight thermal0.070.5
1L785medium thermal0.612
2H736medium thermal0.52
LS refinement shellResolution: 2.852→3.006 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.361 141 -
Rwork0.294 2769 -
obs--97.55 %
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)
11.3872-0.14880.30450.8601-0.68862.67670.12110.16180.04970.004-0.06220.0321-0.09670.064-0.0589-0.001-0.01410.0134-0.0852-0.0072-0.0817-25.4336-12.4619-39.902
21.75950.1060.03610.9692-1.062.4105-0.03640.7507-0.38260.03330.168-0.16130.06940.0106-0.1317-0.1470.00010.01740.2792-0.0808-0.0537.7414-18.659-43.9035
31.1320.3638-0.53880.7395-0.96582.97990.079-0.05440.04070.0472-0.1076-0.0356-0.09140.10430.0286-0.0512-0.0068-0.0027-0.1087-0.0019-0.0501-20.689-30.3438-79.4895
41.962-0.26150.85310.9947-0.40862.44810.09450.0438-0.0464-0.1626-0.01380.18450.2459-0.0007-0.0807-0.0897-0.0043-0.0586-0.30760.0261-0.0865-53.6974-37.8541-81.5308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 123
2X-RAY DIFFRACTION1L1 - 108
3X-RAY DIFFRACTION2H124 - 223
4X-RAY DIFFRACTION2L109 - 212
5X-RAY DIFFRACTION3I1 - 123
6X-RAY DIFFRACTION3M1 - 108
7X-RAY DIFFRACTION4I124 - 222
8X-RAY DIFFRACTION4M109 - 212

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