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- PDB-7xl1: Crystal structure of chimeric 7D12-Vob nanobody at 1.65 Angstrom -

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Basic information

Entry
Database: PDB / ID: 7xl1
TitleCrystal structure of chimeric 7D12-Vob nanobody at 1.65 Angstrom
ComponentsChimeric 7D12-Vob nanobody
KeywordsIMMUNE SYSTEM / nanobody VHH protein engineering protein stability surface plasmon resonance differential scanning calorimetry
Function / homologyMALONATE ION
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCaaveiro, J.M.M. / Kinoshita, S. / Mori, C. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimeric 7D12-Vob nanobody
B: Chimeric 7D12-Vob nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1744
Polymers28,9702
Non-polymers2042
Water2,720151
1
A: Chimeric 7D12-Vob nanobody


Theoretical massNumber of molelcules
Total (without water)14,4851
Polymers14,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chimeric 7D12-Vob nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6893
Polymers14,4851
Non-polymers2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.580, 68.580, 103.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-265-

HOH

21B-366-

HOH

31B-367-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 125 / Label seq-ID: 1 - 125

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

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Components

#1: Antibody Chimeric 7D12-Vob nanobody


Mass: 14484.966 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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium malonate pH 4.0 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: 1.65→35.5 Å / Num. obs: 30042 / % possible obs: 98.8 % / Redundancy: 8.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.038 / Net I/σ(I): 12
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4233 / CC1/2: 0.724 / Rpim(I) all: 0.327 / Rrim(I) all: 0.327 / % possible all: 97.8

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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: 7XL0

7xl0


Resolution: 1.65→35.44 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.006 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1197 4 %RANDOM
Rwork0.156 ---
obs0.158 28821 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 93.48 Å2 / Biso mean: 25.93 Å2 / Biso min: 12.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.02 Å2
Refinement stepCycle: final / Resolution: 1.65→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 14 156 2060
Biso mean--29.76 35.35 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132024
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181783
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.6462759
X-RAY DIFFRACTIONr_angle_other_deg1.3361.5764121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4035271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.68719.907107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76615303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5481519
X-RAY DIFFRACTIONr_chiral_restr0.0630.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_rigid_bond_restr1.35633807
Refine LS restraints NCS

Ens-ID: 1 / Number: 3527 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 78 -
Rwork0.25 2060 -
all-2138 -
obs--97.4 %

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