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- PDB-6ffj: Anti-tumor antibody 14F7-derived single chain fragment variable (scFv) -

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Basic information

Entry
Database: PDB / ID: 6ffj
TitleAnti-tumor antibody 14F7-derived single chain fragment variable (scFv)
Components14F7-derived scFv
KeywordsANTITUMOR PROTEIN / ganglioside / scfv / antibody fragment / single chain fragment variable / immuno therapy / 14F7 / gm3
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBjerregaard-Andersen, K. / Heggelund, J.E. / Krengel, U.
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of an L chain optimised 14F7 anti-ganglioside Fv suggests a unique tumour-specificity through an unusual H-chain CDR3 architecture.
Authors: Bjerregaard-Andersen, K. / Johannesen, H. / Abdel-Rahman, N. / Heggelund, J.E. / Hoas, H.M. / Abraha, F. / Bousquet, P.A. / Hoydahl, L.S. / Burschowsky, D. / Rojas, G. / Oscarson, S. / Loset, G.A. / Krengel, U.
History
DepositionJan 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14F7-derived scFv
C: 14F7-derived scFv
E: 14F7-derived scFv
G: 14F7-derived scFv


Theoretical massNumber of molelcules
Total (without water)112,4654
Polymers112,4654
Non-polymers00
Water4,576254
1
A: 14F7-derived scFv


Theoretical massNumber of molelcules
Total (without water)28,1161
Polymers28,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 14F7-derived scFv


Theoretical massNumber of molelcules
Total (without water)28,1161
Polymers28,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 14F7-derived scFv


Theoretical massNumber of molelcules
Total (without water)28,1161
Polymers28,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 14F7-derived scFv


Theoretical massNumber of molelcules
Total (without water)28,1161
Polymers28,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.798, 119.066, 68.286
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
14F7-derived scFv


Mass: 28116.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Humanized antibody fragment / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFKPEN
Details (production host): co-expresses E. coli chaperone FkpA
Production host: Escherichia coli (E. coli) / Variant (production host): XL1 Blue
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.53 Å3/Da / Density % sol: 51.37 % / Description: Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, 0.02 M 1,6-hexandiol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3- ...Details: 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, 0.02 M 1,6-hexandiol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 0.1 M bicine/tris base pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1,03320
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
233201
ReflectionResolution: 2.2→46.71 Å / Num. obs: 49026 / % possible obs: 94.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 37.78 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.078 / Rrim(I) all: 0.137 / Net I/σ(I): 3.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4880 / CC1/2: 0.8 / Rpim(I) all: 0.374 / Rrim(I) all: 0.653 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MxCuBEdata collection
EDNAdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UMT

3umt


Resolution: 2.2→46.708 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 2495 5.14 %Random
Rwork0.1836 ---
obs0.1865 48584 93.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7194 0 0 254 7448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017368
X-RAY DIFFRACTIONf_angle_d1.06510001
X-RAY DIFFRACTIONf_dihedral_angle_d15.7922673
X-RAY DIFFRACTIONf_chiral_restr0.0651078
X-RAY DIFFRACTIONf_plane_restr0.0061273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24230.35291370.29172468X-RAY DIFFRACTION93
2.2423-2.28810.32551460.2652635X-RAY DIFFRACTION95
2.2881-2.33780.32781620.25122471X-RAY DIFFRACTION93
2.3378-2.39220.32761500.23982530X-RAY DIFFRACTION94
2.3922-2.4520.29281460.23322565X-RAY DIFFRACTION94
2.452-2.51830.27511220.22882557X-RAY DIFFRACTION94
2.5183-2.59240.29111100.22972562X-RAY DIFFRACTION93
2.5924-2.67610.27781540.21012587X-RAY DIFFRACTION95
2.6761-2.77170.28151220.20652595X-RAY DIFFRACTION96
2.7717-2.88270.27971630.20372567X-RAY DIFFRACTION95
2.8827-3.01390.23521240.21132639X-RAY DIFFRACTION95
3.0139-3.17270.30131300.20622541X-RAY DIFFRACTION94
3.1727-3.37150.27551270.20442650X-RAY DIFFRACTION96
3.3715-3.63170.2571530.18082557X-RAY DIFFRACTION94
3.6317-3.9970.19451510.16472572X-RAY DIFFRACTION94
3.997-4.57490.18791360.13752548X-RAY DIFFRACTION93
4.5749-5.76220.17661320.1282542X-RAY DIFFRACTION93
5.7622-46.71890.18531300.16472503X-RAY DIFFRACTION90

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