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- PDB-1moe: The three-dimensional structure of an engineered scFv T84.66 dime... -

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Basic information

Entry
Database: PDB / ID: 1moe
TitleThe three-dimensional structure of an engineered scFv T84.66 dimer or diabody in VL to VH linkage.
Componentsanti-CEA mAb T84.66
KeywordsIMMUNE SYSTEM / anti carcinoembryonic antigen / T84.66 / diabody / dimer / scFv / variable domain
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Ig kappa chain V-III region PC 3741/TEPC 111 / V(H) region of G5 Bb 2.2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCarmichael, J.A. / Power, B.E. / Garrett, T.P.J. / Yazaki, P.J. / Shively, J.E. / Raubischek, A.A. / Wu, A.M. / Hudson, P.J.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The Crystal Structure of an Anti-CEA scFv Diabody Assembled from T84.66 scFvs in VL-to-VH Orientation: Implications for Diabody Flexibility
Authors: Carmichael, J.A. / Power, B.E. / Garrett, T.P. / Yazaki, P.J. / Shively, J.E. / Raubischek, A.A. / Wu, A.M. / Hudson, P.J.
#1: Journal: J.Immunol.Methods / Year: 2001
Title: Mammalian expression and hollow fiber bioreactor production of recombinant anti-CEA diabody and minibody for clinical applications.
Authors: Yazaki, P.J. / Shively, L. / Clark, C. / Cheung, C.W. / Le, W. / Szpikowska, B. / Shively, J.E. / Raubitschek, A.A. / Wu, A.M.
#2: Journal: Acta Crystallogr.,Sect.A / Year: 1999
Title: Structure of an Exoglucanase complexed with conduritol B epoxide from A 50um Crystal using monocappilary optics.
Authors: Varghese, L.N. / Van Donkelaar, A. / Hrmova, M. / Fincher, G.A. / Baliac, D.X. / Barnia, Z.
History
DepositionSep 9, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 25, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: anti-CEA mAb T84.66
B: anti-CEA mAb T84.66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9195
Polymers51,6312
Non-polymers2883
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-56 kcal/mol
Surface area20950 Å2
MethodPISA
2
A: anti-CEA mAb T84.66
B: anti-CEA mAb T84.66
hetero molecules

A: anti-CEA mAb T84.66
B: anti-CEA mAb T84.66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,83910
Polymers103,2624
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area12250 Å2
ΔGint-126 kcal/mol
Surface area37630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.314, 64.314, 247.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody anti-CEA mAb T84.66 / T84.66 Anti-CEA SCFV Dimer


Mass: 25815.623 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-240
Source method: isolated from a genetically manipulated source
Details: immunoglobulin variable domains linked VL to VH with (GGGSGGGG)
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pEE12 / Cell (production host): myeloma NSO cells / Gene (production host): T84.66 / Production host: Mus musculus (house mouse)
References: UniProt: P01660, GenBank: 50373, UniProt: Q5R3X1*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: sodium chloride, HEPES, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
30.1 M1reservoirNaCl
41.6 Mammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEAug 25, 1999micro capillary focussing optic
RIGAKU RAXIS IV2IMAGE PLATEOct 4, 1999micro capillary focussing optic
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1micro capillary focussing opticSINGLE WAVELENGTHMx-ray1
2micro capillary focussing opticSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 19293 / Num. obs: 17303 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 14.2 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 18 / Limit k min: 0 / Limit l max: 96 / Limit l min: 0 / Observed criterion F max: 322511.49 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1347 / % possible all: 72
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 15066 / % possible obs: 86.2 % / Redundancy: 52.4 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 44.2 % / Redundancy: 18.5 % / Num. unique obs: 819 / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassificationNB
CNS1refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gg2

1gg2


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1251 7.9 %random
Rwork0.213 ---
all0.246 19145 --
obs0.243 15856 82.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 35.2171 Å2 / ksol: 0.30081 e/Å3
Displacement parametersBiso max: 104.15 Å2 / Biso mean: 42.58 Å2 / Biso min: 10.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.836 Å20 Å20 Å2
2---2.836 Å20 Å2
3---5.672 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.56 Å
Luzzati d res high-2.49
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 15 71 3722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_torsion_deg27.1
X-RAY DIFFRACTIONx_torsion_impr_deg1.26
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.49-2.580.446743.90.45210320.0521875110659
2.58-2.680.3771095.80.38211820.0361865129169.2
2.68-2.80.3281538.20.32913570.0261866151080.9
2.8-2.950.3071457.70.30814980.0261871164387.8
2.95-3.140.2921166.20.28715730.0271883168989.7
3.14-3.380.2981256.60.29215380.0271906166387.2
3.38-3.710.2641216.40.25415000.0241890162185.8
3.71-4.250.2391226.30.22814760.0221934159882.6
4.25-5.330.1831256.30.17815780.0161975170386.2
5.33-19.890.2581617.70.2618710.022088203297.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4so4_xplor.paramso4_xplor.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1

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