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- PDB-6y1r: Nb22-LBT -

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Basic information

Entry
Database: PDB / ID: 6y1r
TitleNb22-LBT
ComponentsNb22-LBT
KeywordsIMMUNE SYSTEM / Nanobody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TERBIUM(III) ION
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Nb22-LBT
B: Nb22-LBT
C: Nb22-LBT
D: Nb22-LBT
E: Nb22-LBT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,40020
Polymers80,3935
Non-polymers2,00715
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-179 kcal/mol
Surface area32420 Å2
Unit cell
Length a, b, c (Å)45.469, 49.425, 81.349
Angle α, β, γ (deg.)91.710, 99.180, 102.610
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nb22-LBT


Mass: 16078.619 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
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.: 9 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 22% PEG5000MME 0.1 M MES pH 6.5 0.2 M Ammonium sulfate

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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: 1.6494 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6494 Å / Relative weight: 1
ReflectionResolution: 1.73→80.13 Å / Num. obs: 63824 / % possible obs: 90 % / Redundancy: 6.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.093 / Rrim(I) all: 0.248 / Net I/σ(I): 8.4 / Num. measured all: 433861
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
1.73-1.765.52.6581023918570.1681.1832.9240.847.2
8.99-80.137.60.17738095020.9860.0680.1892399.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
Aimless0.5.32data scaling
SHELXDEphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.85→80.127 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 2731 5.04 %
Rwork0.2042 51436 -
obs0.2057 54167 93.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.98 Å2 / Biso mean: 40.9121 Å2 / Biso min: 11.51 Å2
Refinement stepCycle: final / Resolution: 1.85→80.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 39 316 5542
Biso mean--42.45 40.11 -
Num. residues----685
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.88190.31181290.2771246189
1.8819-1.91610.25571280.2637251391
1.9161-1.9530.29251310.2436244189
1.953-1.99290.29051220.2411253691
1.9929-2.03620.26871460.2324252592
2.0362-2.08360.25161310.2263250491
2.0836-2.13570.27611440.229256493
2.1357-2.19340.25721090.2187251090
2.1934-2.2580.25661100.2067259693
2.258-2.33090.2461680.2117254194
2.3309-2.41420.21381320.2107256193
2.4142-2.51080.24671570.2117257894
2.5108-2.62510.24921440.2129260494
2.6251-2.76350.2481530.2146254593
2.7635-2.93670.25081510.2143265396
2.9367-3.16340.29411340.2106263596
3.1634-3.48180.23421400.1988266695
3.4818-3.98560.22071140.1843262895
3.9856-5.02130.161520.1652270798
5.0213-80.1270.23271360.2053266897

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