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- PDB-7nx2: Unbound antigen-binding fragment (FAb) 324 -

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Basic information

Entry
Database: PDB / ID: 7nx2
TitleUnbound antigen-binding fragment (FAb) 324
Components
  • FAb 324 Heavy Chain
  • FAb 324 Light Chain
KeywordsPROTEIN BINDING / Antibody
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsDe Munck, S. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Nature / Year: 2021
Title: Structural basis of cytokine-mediated activation of ALK family receptors.
Authors: De Munck, S. / Provost, M. / Kurikawa, M. / Omori, I. / Mukohyama, J. / Felix, J. / Bloch, Y. / Abdel-Wahab, O. / Bazan, J.F. / Yoshimi, A. / Savvides, S.N.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAb 324 Light Chain
B: FAb 324 Heavy Chain
C: FAb 324 Light Chain
D: FAb 324 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,54211
Polymers96,8694
Non-polymers6727
Water14,394799
1
A: FAb 324 Light Chain
B: FAb 324 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9157
Polymers48,4352
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-88 kcal/mol
Surface area19110 Å2
MethodPISA
2
C: FAb 324 Light Chain
D: FAb 324 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6274
Polymers48,4352
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-53 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.240, 87.090, 126.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

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
111ASPASPTHRTHR(chain 'A' and (resid 1 through 197 or resid 199 through 216))AA1 - 1971 - 197
121GLUGLUTHRTHR(chain 'A' and (resid 1 through 197 or resid 199 through 216))AA199 - 201199 - 201
131PROPROASNASN(chain 'A' and (resid 1 through 197 or resid 199 through 216))AA208 - 216208 - 216
241ASPASPTHRTHR(chain 'C' and (resid 1 through 197 or resid 199 through 201 or resid 208 through 216))CC1 - 1971 - 197
251GLUGLUTHRTHR(chain 'C' and (resid 1 through 197 or resid 199 through 201 or resid 208 through 216))CC199 - 201199 - 201
261PROPROASNASN(chain 'C' and (resid 1 through 197 or resid 199 through 201 or resid 208 through 216))CC208 - 216208 - 216
172GLNGLNPHEPHE(chain 'B' and (resid 0 through 28 or resid 31 through 100 or resid 103 through 220))BB0 - 281 - 29
182TYRTYRARGARG(chain 'B' and (resid 0 through 28 or resid 31 through 100 or resid 103 through 220))BB31 - 9932 - 100
192TYRTYRSERSER(chain 'B' and (resid 0 through 28 or resid 31 through 100 or resid 103 through 220))BB103 - 135104 - 136
1102SERSERARGARG(chain 'B' and (resid 0 through 28 or resid 31 through 100 or resid 103 through 220))BB141 - 220142 - 221
2112GLNGLNPHEPHE(chain 'D' and (resid 0 through 28 or resid 31 through 100 or resid 103 through 220))DD0 - 281 - 29
2122TYRTYRARGARG(chain 'D' and (resid 0 through 28 or resid 31 through 100 or resid 103 through 220))DD31 - 9932 - 100
2132TYRTYRSERSER(chain 'D' and (resid 0 through 28 or resid 31 through 100 or resid 103 through 220))DD103 - 135104 - 136
2142SERSERARGARG(chain 'D' and (resid 0 through 28 or resid 31 through 100 or resid 103 through 220))DD141 - 220142 - 221

NCS ensembles :
ID
1
2

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Components

#1: Antibody FAb 324 Light Chain


Mass: 23918.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody FAb 324 Heavy Chain


Mass: 24516.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 1.5M (NH4)2SO4 40 mM Glycine pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.47→71.76 Å / Num. obs: 147145 / % possible obs: 99.2 % / Redundancy: 3.82 % / Biso Wilson estimate: 16.19 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.04 / Net I/σ(I): 17.32
Reflection shellResolution: 1.47→1.56 Å / Num. unique obs: 19382 / CC1/2: 0.42 / Rrim(I) all: 0.39 / % possible all: 79

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NUZ

5nuz


Resolution: 1.47→43.55 Å / SU ML: 0.1417 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 1827 1.24 %RANDOM
Rwork0.1679 145099 --
obs0.1684 146926 96.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.34 Å2
Refinement stepCycle: LAST / Resolution: 1.47→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 35 799 7363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796754
X-RAY DIFFRACTIONf_angle_d1.02499196
X-RAY DIFFRACTIONf_chiral_restr0.08681009
X-RAY DIFFRACTIONf_plane_restr0.00621172
X-RAY DIFFRACTIONf_dihedral_angle_d12.23292394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.510.30171070.24048182X-RAY DIFFRACTION71.26
1.51-1.550.24741110.20839848X-RAY DIFFRACTION85.49
1.55-1.60.21911520.18811388X-RAY DIFFRACTION99.41
1.6-1.660.2381400.178111474X-RAY DIFFRACTION99.79
1.66-1.730.21191380.172511499X-RAY DIFFRACTION99.39
1.73-1.810.21821480.162711420X-RAY DIFFRACTION99.01
1.81-1.90.19241550.154811503X-RAY DIFFRACTION99.85
1.9-2.020.22531310.154311562X-RAY DIFFRACTION99.7
2.02-2.180.19981410.151311396X-RAY DIFFRACTION98.45
2.18-2.40.21441550.156111586X-RAY DIFFRACTION99.82
2.4-2.740.17041460.16811577X-RAY DIFFRACTION99.2
2.74-3.460.17751510.168311703X-RAY DIFFRACTION99.75
3.46-43.550.22411520.172511961X-RAY DIFFRACTION98.66

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