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- PDB-6xym: Nbe-LBM -

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Basic information

Entry
Database: PDB / ID: 6xym
TitleNbe-LBM
ComponentsNbe-LBM
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: 1.2 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
DepositionJan 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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)31,4824
Polymers31,1642
Non-polymers3182
Water3,477193
1
A: Nbe-LBM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7412
Polymers15,5821
Non-polymers1591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nbe-LBM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7412
Polymers15,5821
Non-polymers1591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.731, 63.855, 66.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

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Components

#1: Protein Nbe-LBM


Mass: 15582.064 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 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: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→63.85 Å / Num. obs: 81806 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Net I/σ(I): 15.9 / Num. measured all: 1061978
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
1.2-1.2212.33.3724904539730.5180.9863.5170.898.7
6.57-63.8512.10.04871445910.9990.0140.0572.399.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSVERSION Jan 26, 2018data reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→60.73 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1949 / WRfactor Rwork: 0.1458 / FOM work R set: 0.7203 / SU B: 2.492 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0385 / SU Rfree: 0.0422 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 4045 4.9 %RANDOM
Rwork0.1539 ---
obs0.1562 77705 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 178.26 Å2 / Biso mean: 32.637 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å20 Å20 Å2
2--1.68 Å20 Å2
3---1.4 Å2
Refinement stepCycle: final / Resolution: 1.2→60.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 2 193 2238
Biso mean--19.92 39.73 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132221
X-RAY DIFFRACTIONr_bond_other_d0.0050.0181965
X-RAY DIFFRACTIONr_angle_refined_deg2.0731.6343011
X-RAY DIFFRACTIONr_angle_other_deg1.6671.5924554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.255.066302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.05421.855124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94415360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7111518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022655
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02519
X-RAY DIFFRACTIONr_rigid_bond_restr11.33934182
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 282 -
Rwork0.312 5672 -
all-5954 -
obs--99.13 %

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