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- PDB-6y0e: Nbe LBM -

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Basic information

Entry
Database: PDB / ID: 6y0e
TitleNbe LBM
ComponentsNBe-LBM
KeywordsIMMUNE SYSTEM / Nanobody
Function / homologyTERBIUM(III) ION
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsPompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T.
CitationJournal: To Be Published
Title: Engineered nanobodies with a lanthanide binding motif for crystallographic phasing
Authors: Pompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T.
History
DepositionFeb 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NBe-LBM
B: NBe-LBM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0424
Polymers29,7242
Non-polymers3182
Water3,351186
1
A: NBe-LBM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0212
Polymers14,8621
Non-polymers1591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NBe-LBM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0212
Polymers14,8621
Non-polymers1591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.477, 50.612, 93.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NBe-LBM


Mass: 14862.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NBe-LBM / Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.77 Å3/Da / Density % sol: 30.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30 %(w/v) PEG 1500

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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: 1.0032 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0032 Å / Relative weight: 1
ReflectionResolution: 1.5→50.61 Å / Num. obs: 34335 / % possible obs: 99.3 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Net I/σ(I): 22.1 / Num. measured all: 443937
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.5312.20.9522008916440.7740.2790.9932.898.1
8.22-50.6110.90.03729452710.9990.0110.03967.299.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.11data scaling
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→46.764 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.62
RfactorNum. reflection% reflection
Rfree0.1803 1713 5 %
Rwork0.1608 --
obs0.1618 34277 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.78 Å2 / Biso mean: 22.398 Å2 / Biso min: 8.42 Å2
Refinement stepCycle: final / Resolution: 1.5→46.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 2 186 2168
Biso mean--17.85 31.12 -
Num. residues----253
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.54410.29261420.2182260698
1.5441-1.5940.22761340.1966269899
1.594-1.6510.23711310.1786265699
1.651-1.71710.20341430.172267699
1.7171-1.79520.20981400.1615267999
1.7952-1.88990.18881260.1506268799
1.8899-2.00830.15251360.1422272299
2.0083-2.16330.17581600.14432694100
2.1633-2.3810.19731550.14772701100
2.381-2.72550.16931500.1507273599
2.7255-3.43370.16241470.16332789100
3.4337-46.7640.16991490.16752921100

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