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- PDB-5nlw: Structure of Nb36 crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 5nlw
TitleStructure of Nb36 crystal form 2
Componentsnanobody Nb36
KeywordsIMMUNE SYSTEM / Ig domain llama single domain antibody nanobody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsHansen, S.B. / Andersen, K.R. / Laursen, N.S. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
The Danish Research Council for Independent ResearchDanscatt Denmark
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Introducing site-specific cysteines into nanobodies for mercury labelling allows de novo phasing of their crystal structures.
Authors: Hansen, S.B. / Laursen, N.S. / Andersen, G.R. / Andersen, K.R.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 15, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nanobody Nb36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6742
Polymers13,5781
Non-polymers961
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area6410 Å2
2
A: nanobody Nb36
hetero molecules

A: nanobody Nb36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3494
Polymers27,1562
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1680 Å2
ΔGint-47 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.860, 30.040, 32.890
Angle α, β, γ (deg.)90.000, 90.840, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody nanobody Nb36


Mass: 13578.210 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 1.85 Å3/Da / Density % sol: 33.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Hepes pH 7.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.5→32.886 Å / Num. obs: 15244 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 3.381 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.063 / Χ2: 1.107 / Net I/σ(I): 10.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.542.6650.77818260.3960.95470.1
1.54-1.582.8950.6491.298930.4990.78675.9
1.58-1.633.0340.5721.5510300.6850.68794.5
1.63-1.683.4210.5271.9110860.770.62397
1.68-1.733.4550.4362.3810460.8640.51498.9
1.73-1.793.5380.3573.2510070.8820.4297.9
1.79-1.863.5430.2544.189670.970.29997.5
1.86-1.943.5420.1836.089350.9710.21696.9
1.94-2.023.550.1328.298920.9880.15597.5
2.02-2.123.5740.11510.618680.9860.13598
2.12-2.233.6150.09613.038080.9880.11397.7
2.23-2.373.5240.08614.427790.9920.10197.7
2.37-2.533.4350.06916.597440.9930.08297.9
2.53-2.743.470.05819.036850.9950.06898.7
2.74-33.4120.0522.046360.9950.05998.1
3-3.353.5510.0426.295640.9970.04797.6
3.35-3.873.3830.03728.314940.9960.04496.9
3.87-4.743.3680.03129.164400.9980.03798
4.74-6.73.4410.0329.463450.9980.03598.3
6.7-32.8863.0950.02828.351990.9980.03397.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→32.886 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.22
RfactorNum. reflection% reflection
Rfree0.2484 1529 10.04 %
Rwork0.1994 --
obs0.2042 15222 93.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.6 Å2 / Biso mean: 45.1498 Å2 / Biso min: 16.28 Å2
Refinement stepCycle: final / Resolution: 1.5→32.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms874 0 5 73 952
Biso mean--29.45 42.72 -
Num. residues----117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002909
X-RAY DIFFRACTIONf_angle_d0.4851238
X-RAY DIFFRACTIONf_chiral_restr0.059141
X-RAY DIFFRACTIONf_plane_restr0.001158
X-RAY DIFFRACTIONf_dihedral_angle_d12.209331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.499-1.54740.3771020.3702925102771
1.5474-1.60270.35121220.34131075119782
1.6027-1.66690.43161420.31851285142797
1.6669-1.74270.26941390.28291294143398
1.7427-1.83460.27831490.25341279142897
1.8346-1.94950.26791470.22571280142797
1.9495-2.10.27651380.20241278141697
2.1-2.31130.23451470.19961306145398
2.3113-2.64570.2281470.2081296144398
2.6457-3.33280.24291430.19661324146798
3.3328-32.89440.22941530.16411351150498
Refinement TLS params.Method: refined / Origin x: -15.1409 Å / Origin y: -9.2688 Å / Origin z: 13.8157 Å
111213212223313233
T0.2016 Å20.0048 Å20.0239 Å2-0.1589 Å20.0007 Å2--0.2039 Å2
L3.0177 °20.2655 °20.4379 °2-2.9367 °2-0.6447 °2--2.0573 °2
S0.0352 Å °0.0632 Å °-0.216 Å °-0.0333 Å °-0.0436 Å °-0.3661 Å °0.0468 Å °0.3302 Å °-0.0118 Å °
Refinement TLS groupSelection details: chain A

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