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- PDB-6jri: Crystal structure of Nanobody -

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Basic information

Entry
Database: PDB / ID: 6jri
TitleCrystal structure of Nanobody
ComponentsNanobody
KeywordsANTIVIRAL PROTEIN / Nanobody / therapeutic
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.101 Å
AuthorsMo, X. / Li, J. / Xu, X. / Yuan, A.Y.
CitationJournal: To Be Published
Title: Crystal structure of nanobody at 3.1 Angstroms resolution.
Authors: Mo, X.
History
DepositionApr 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nanobody
A: Nanobody
C: Nanobody
D: Nanobody
E: Nanobody
F: Nanobody
G: Nanobody
H: Nanobody


Theoretical massNumber of molelcules
Total (without water)114,4948
Polymers114,4948
Non-polymers00
Water724
1
A: Nanobody
C: Nanobody

B: Nanobody
G: Nanobody


Theoretical massNumber of molelcules
Total (without water)57,2474
Polymers57,2474
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area3770 Å2
ΔGint-22 kcal/mol
Surface area23820 Å2
MethodPISA
2
D: Nanobody
E: Nanobody
F: Nanobody
H: Nanobody


Theoretical massNumber of molelcules
Total (without water)57,2474
Polymers57,2474
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-22 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.305, 85.471, 229.145
Angle α, β, γ (deg.)90.00, 91.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
Nanobody


Mass: 14311.781 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 280 K / Method: evaporation / Details: 0.1 M sodium Acetate, 2.0 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.101→29.715 Å / Num. obs: 25640 / % possible obs: 93.92 % / Redundancy: 2.8 % / Net I/σ(I): 15.54
Reflection shellResolution: 3.101→3.212 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.101→29.715 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 2003 8.59 %
Rwork0.2353 --
obs0.2374 23318 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.101→29.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7696 0 0 4 7700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037877
X-RAY DIFFRACTIONf_angle_d0.79210652
X-RAY DIFFRACTIONf_dihedral_angle_d4.2644468
X-RAY DIFFRACTIONf_chiral_restr0.0431110
X-RAY DIFFRACTIONf_plane_restr0.0071350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1013-3.17880.31321400.29051504X-RAY DIFFRACTION94
3.1788-3.26470.3311530.25631587X-RAY DIFFRACTION97
3.2647-3.36060.26691420.241530X-RAY DIFFRACTION97
3.3606-3.46890.28321440.24381596X-RAY DIFFRACTION97
3.4689-3.59270.26171440.25331512X-RAY DIFFRACTION97
3.5927-3.73630.24281490.24451593X-RAY DIFFRACTION97
3.7363-3.9060.30021440.24461568X-RAY DIFFRACTION96
3.906-4.11140.27491430.23521503X-RAY DIFFRACTION95
4.1114-4.36820.2631320.22221467X-RAY DIFFRACTION91
4.3682-4.70430.22211380.19361429X-RAY DIFFRACTION87
4.7043-5.17550.21011360.2161443X-RAY DIFFRACTION90
5.1755-5.91920.22711440.23491528X-RAY DIFFRACTION94
5.9192-7.43820.28951450.25691547X-RAY DIFFRACTION95
7.4382-29.71640.25771490.23371508X-RAY DIFFRACTION90

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