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- PDB-7vsw: Crystal structure of a Fab-like fragment of anti-mesothelin antibody -

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Basic information

Entry
Database: PDB / ID: 7vsw
TitleCrystal structure of a Fab-like fragment of anti-mesothelin antibody
Components
  • heavy chain
  • light chain
KeywordsBIOSYNTHETIC PROTEIN / antibody / therapeutic
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYang, Z. / Ying, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070938 China
CitationJournal: Small Methods / Year: 2022
Title: Design of a Novel Fab-Like Antibody Fragment with Enhanced Stability and Affinity for Clinical use.
Authors: Wang, C. / Hong, J. / Yang, Z. / Zhou, X. / Yang, Y. / Kong, Y. / Chen, B. / Wu, H. / Qian, B.Z. / Dimitrov, D.S. / Zhou, X. / Wu, Y. / Ying, T.
History
DepositionOct 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: light chain
B: heavy chain
E: light chain
F: heavy chain
I: light chain
J: heavy chain
M: light chain
N: heavy chain


Theoretical massNumber of molelcules
Total (without water)197,4118
Polymers197,4118
Non-polymers00
Water00
1
A: light chain
B: heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3532
Polymers49,3532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-22 kcal/mol
Surface area20290 Å2
MethodPISA
2
E: light chain
F: heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3532
Polymers49,3532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-22 kcal/mol
Surface area20020 Å2
MethodPISA
3
I: light chain
J: heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3532
Polymers49,3532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-23 kcal/mol
Surface area20000 Å2
MethodPISA
4
M: light chain
N: heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3532
Polymers49,3532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-23 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.900, 143.900, 261.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLUGLU(chain 'A' and (resid 1 through 106 or resid 109 through 211))AA1 - 1051 - 105
121GLNGLNLEULEU(chain 'A' and (resid 1 through 106 or resid 109 through 211))AA109 - 210109 - 210
231ASPASPGLUGLU(chain 'E' and (resid 1 through 106 or resid 109 through 211))EC1 - 1051 - 105
241GLNGLNLEULEU(chain 'E' and (resid 1 through 106 or resid 109 through 211))EC109 - 210109 - 210
351ASPASPGLUGLU(chain 'I' and (resid 1 through 106 or resid 109 through 211))IE1 - 1051 - 105
361GLNGLNLEULEU(chain 'I' and (resid 1 through 106 or resid 109 through 211))IE109 - 210109 - 210
471ASPASPGLUGLU(chain 'M' and (resid 1 through 106 or resid 109 through 211))MG1 - 1051 - 105
481GLNGLNLEULEU(chain 'M' and (resid 1 through 106 or resid 109 through 211))MG109 - 210109 - 210
192GLNGLNLEULEU(chain 'B' and resid 1 through 223)BB1 - 2221 - 222
2102GLNGLNLEULEUchain 'F'FD1 - 2221 - 222
3112GLNGLNLEULEUchain 'J'JF1 - 2221 - 222
4122GLNGLNLEULEUchain 'N'NH1 - 2221 - 222

NCS ensembles :
ID
1
2

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Components

#1: Antibody
light chain


Mass: 23726.393 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody
heavy chain


Mass: 25626.424 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
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: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4.0 M sodium chloride and 0.1 M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→28.22 Å / Num. obs: 55749 / % possible obs: 99.9 % / Redundancy: 26.6 % / Biso Wilson estimate: 84.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.201 / Net I/σ(I): 17.4
Reflection shellResolution: 3→3.08 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4039 / CC1/2: 0.75 / Rpim(I) all: 0.722 / Χ2: 0.97

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CNR

6cnr


Resolution: 3→21.17 Å / SU ML: 0.4201 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2525 2818 5.08 %
Rwork0.2165 52616 -
obs0.2183 55434 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.62 Å2
Refinement stepCycle: LAST / Resolution: 3→21.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13508 0 0 0 13508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002613861
X-RAY DIFFRACTIONf_angle_d0.63218872
X-RAY DIFFRACTIONf_chiral_restr0.04332062
X-RAY DIFFRACTIONf_plane_restr0.00392424
X-RAY DIFFRACTIONf_dihedral_angle_d2.22968250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.050.38961350.34382589X-RAY DIFFRACTION99.85
3.05-3.110.40061620.32692551X-RAY DIFFRACTION99.89
3.11-3.170.36821430.32332586X-RAY DIFFRACTION99.71
3.17-3.230.3721220.31232605X-RAY DIFFRACTION99.53
3.23-3.30.34961230.30342607X-RAY DIFFRACTION99.67
3.3-3.380.39711440.29682567X-RAY DIFFRACTION99.71
3.38-3.460.30871340.26332619X-RAY DIFFRACTION99.71
3.46-3.550.30931380.26162603X-RAY DIFFRACTION99.78
3.55-3.660.27621590.25622583X-RAY DIFFRACTION99.53
3.66-3.780.31141490.25392625X-RAY DIFFRACTION99.96
3.78-3.910.25691390.24072604X-RAY DIFFRACTION99.75
3.91-4.070.25081330.22792617X-RAY DIFFRACTION99.82
4.07-4.250.26061320.20462636X-RAY DIFFRACTION99.75
4.25-4.470.23261520.19062634X-RAY DIFFRACTION99.86
4.47-4.750.18821370.17812625X-RAY DIFFRACTION99.75
4.75-5.110.19071560.1692645X-RAY DIFFRACTION99.75
5.11-5.620.23091420.17842645X-RAY DIFFRACTION99.75
5.62-6.410.21661310.19172702X-RAY DIFFRACTION99.72
6.41-80.23581450.19492734X-RAY DIFFRACTION99.83
8-21.170.20791420.18652839X-RAY DIFFRACTION99.4

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