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- PDB-5nlu: Structure of Nb36 crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 5nlu
TitleStructure of Nb36 crystal form 1
Componentssingle domain llama antibody 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: 1.193 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 / reflns_shell
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 / _reflns_shell.percent_possible_all
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: single domain llama antibody Nb36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6742
Polymers13,5781
Non-polymers961
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area6430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.560, 29.270, 33.130
Angle α, β, γ (deg.)90.000, 97.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

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Components

#1: Antibody single domain llama antibody 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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.96 Å3/Da / Density % sol: 37.11 %
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: Diamond / Beamline: I02 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.19→32.882 Å / Num. obs: 30669 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6.646 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.091 / Χ2: 1.047 / Net I/σ(I): 10.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.19-1.224.1141.0521.0817140.3951.19474.1
1.22-1.265.4150.9881.3821340.6021.09596.7
1.26-1.296.3150.8291.8922170.7340.906100
1.29-1.337.020.7212.421220.820.7899.6
1.33-1.387.0660.5842.9820420.9030.631100
1.38-1.437.0330.4653.8119800.9340.503100
1.43-1.487.0220.3295.2919290.9670.356100
1.48-1.547.0320.2596.7718620.9770.2899.9
1.54-1.617.0110.2028.6317780.9850.219100
1.61-1.696.9340.15910.8516870.9890.17299.8
1.69-1.786.7820.13212.8316160.990.14499.6
1.78-1.896.7960.1115.7515160.9930.1299.9
1.89-2.026.9730.09419.7514570.9950.10299.7
2.02-2.186.8590.08221.9913400.9950.08999.8
2.18-2.397.0280.08223.8312450.9960.08999.9
2.39-2.677.1250.08725.5611330.9940.09599.6
2.67-3.087.0060.07826.789910.9940.08599.7
3.08-3.776.7850.06228.228520.9950.06899.5
3.77-5.346.7140.05129.126650.9980.05699.4
5.34-32.8826.5660.04628.493890.9980.0599.7

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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: 1.193→32.882 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.34
RfactorNum. reflection% reflection
Rfree0.1979 1998 6.52 %
Rwork0.175 --
obs0.1765 30642 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.65 Å2 / Biso mean: 23.4335 Å2 / Biso min: 9.19 Å2
Refinement stepCycle: final / Resolution: 1.193→32.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 5 139 1027
Biso mean--20.31 29.37 -
Num. residues----118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008925
X-RAY DIFFRACTIONf_angle_d1.0271261
X-RAY DIFFRACTIONf_chiral_restr0.081143
X-RAY DIFFRACTIONf_plane_restr0.006162
X-RAY DIFFRACTIONf_dihedral_angle_d13.811338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1931-1.22290.60521070.47611534164173
1.2229-1.2560.49851380.40981967210596
1.256-1.29290.30441460.325120962242100
1.2929-1.33460.30681450.269420672212100
1.3346-1.38230.23451460.238120912237100
1.3823-1.43770.2631430.221220582201100
1.4377-1.50310.24151440.205720832227100
1.5031-1.58240.23091450.195220722217100
1.5824-1.68150.20411470.171721022249100
1.6815-1.81130.20331450.168920882233100
1.8113-1.99360.18841460.154720992245100
1.9936-2.2820.16851460.151420902236100
2.282-2.87480.16971480.163121192267100
2.8748-32.89480.17331520.151721782330100
Refinement TLS params.Method: refined / Origin x: -16.6947 Å / Origin y: -10.634 Å / Origin z: 14.2734 Å
111213212223313233
T0.11 Å2-0.0046 Å20.0022 Å2-0.1137 Å20.0008 Å2--0.1111 Å2
L2.3952 °20.0496 °20.3955 °2-1.456 °2-0.1027 °2--0.8519 °2
S-0.0215 Å °0.0338 Å °-0.0303 Å °0.029 Å °0.0064 Å °-0.1616 Å °-0.0161 Å °0.1148 Å °0.0051 Å °
Refinement TLS groupSelection details: chain A

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