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- PDB-7xl0: Crystal structure of Vobarilizumab at 1.70 Angstrom -

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Basic information

Entry
Database: PDB / ID: 7xl0
TitleCrystal structure of Vobarilizumab at 1.70 Angstrom
ComponentsNanobody Vobarilizumab
KeywordsIMMUNE SYSTEM / nanobody VHH protein engineering protein stability surface plasmon resonance differential scanning calorimetry
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCaaveiro, J.M.M. / Mori, C. / Kinoshita, S. / Nakakido, M. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Protein Sci. / Year: 2022
Title: Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3.
Authors: Kinoshita, S. / Nakakido, M. / Mori, C. / Kuroda, D. / Caaveiro, J.M.M. / Tsumoto, K.
History
DepositionApr 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 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

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Assembly

Deposited unit
A: Nanobody Vobarilizumab
B: Nanobody Vobarilizumab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4465
Polymers28,1612
Non-polymers2843
Water3,387188
1
A: Nanobody Vobarilizumab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3654
Polymers14,0811
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area6640 Å2
MethodPISA
2
B: Nanobody Vobarilizumab


Theoretical massNumber of molelcules
Total (without water)14,0811
Polymers14,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.591, 56.420, 42.240
Angle α, β, γ (deg.)90.000, 101.920, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 3 - 120 / Label seq-ID: 3 - 120

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Antibody Nanobody Vobarilizumab


Mass: 14080.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium sulfate 20% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→52 Å / Num. obs: 31315 / % possible obs: 98.9 % / Redundancy: 6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Net I/σ(I): 11.5
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 4232 / CC1/2: 0.89 / Rpim(I) all: 0.16

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVG

5hvg


Resolution: 1.7→51.25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.876 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 1275 4.1 %RANDOM
Rwork0.1521 ---
obs0.1539 30038 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.97 Å2 / Biso mean: 25.895 Å2 / Biso min: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.29 Å2
2--0.01 Å20 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.7→51.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 16 188 2018
Biso mean--33.71 34.58 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131918
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181759
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.6392611
X-RAY DIFFRACTIONr_angle_other_deg1.2951.5744077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3635258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84920.83396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25915316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4791516
X-RAY DIFFRACTIONr_chiral_restr0.0580.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
X-RAY DIFFRACTIONr_rigid_bond_restr1.11333677
Refine LS restraints NCS

Ens-ID: 1 / Number: 3227 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 76 -
Rwork0.21 1897 -
all-1973 -
obs--85.67 %

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