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- PDB-5nm0: Nb36 Ser85Cys with Hg, crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 5nm0
TitleNb36 Ser85Cys with Hg, crystal form 1
ComponentsNb36
KeywordsIMMUNE SYSTEM / Ig domain llama single domain antibody nanobody Hg derivative
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.0Jun 7, 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 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nb36
B: Nb36
C: Nb36
D: Nb36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7786
Polymers54,3774
Non-polymers4012
Water6,828379
1
A: Nb36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7952
Polymers13,5941
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-16 kcal/mol
Surface area6260 Å2
MethodPISA
2
B: Nb36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7952
Polymers13,5941
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-16 kcal/mol
Surface area6260 Å2
MethodPISA
3
C: Nb36


Theoretical massNumber of molelcules
Total (without water)13,5941
Polymers13,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5910 Å2
MethodPISA
4
D: Nb36


Theoretical massNumber of molelcules
Total (without water)13,5941
Polymers13,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.610, 93.070, 142.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 22 or resid 24...
21(chain B and (resid 3 through 22 or resid 24...
31(chain C and (resid 3 through 22 or resid 24 through 95 or resid 97 through 118))
41(chain D and (resid 3 through 22 or resid 24...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSER(chain A and (resid 3 through 22 or resid 24...AA3 - 223 - 22
12VALVALPHEPHE(chain A and (resid 3 through 22 or resid 24...AA24 - 9524 - 95
13ASNASNTHRTHR(chain A and (resid 3 through 22 or resid 24...AA97 - 10297 - 102
14VALVALSERSER(chain A and (resid 3 through 22 or resid 24...AA108 - 118108 - 118
21VALVALSERSER(chain B and (resid 3 through 22 or resid 24...BB3 - 223 - 22
22VALVALPHEPHE(chain B and (resid 3 through 22 or resid 24...BB24 - 9524 - 95
23ASNASNTHRTHR(chain B and (resid 3 through 22 or resid 24...BB97 - 10297 - 102
24VALVALSERSER(chain B and (resid 3 through 22 or resid 24...BB108 - 118108 - 118
31VALVALSERSER(chain C and (resid 3 through 22 or resid 24 through 95 or resid 97 through 118))CC3 - 223 - 22
32VALVALPHEPHE(chain C and (resid 3 through 22 or resid 24 through 95 or resid 97 through 118))CC24 - 9524 - 95
33ASNASNSERSER(chain C and (resid 3 through 22 or resid 24 through 95 or resid 97 through 118))CC97 - 11897 - 118
41VALVALSERSER(chain D and (resid 3 through 22 or resid 24...DD3 - 223 - 22
42VALVALPHEPHE(chain D and (resid 3 through 22 or resid 24...DD24 - 9524 - 95
43ASNASNTHRTHR(chain D and (resid 3 through 22 or resid 24...DD97 - 10297 - 102
44VALVALSERSER(chain D and (resid 3 through 22 or resid 24...DD108 - 118108 - 118

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Components

#1: Antibody
Nb36


Mass: 13594.275 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M Citric acid, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.5→71.255 Å / Num. obs: 153776 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.39 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.054 / Net I/σ(I): 12.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.543.321.0751.06113320.451.2999.5
1.54-1.583.50.7881.51108540.630.93999.6
1.58-1.633.50.6331.97108540.750.7599.6
1.63-1.683.430.4872.51104770.830.57699.6
1.68-1.733.310.3653.3101950.890.4399.7
1.73-1.793.20.264.498930.930.3199.6
1.79-1.863.550.1885.894410.960.2399.5
1.86-1.943.550.1438.291480.9810.16899.5
1.94-2.023.520.10311.187280.9880.12299.5
2.02-2.123.480.08413.483840.9910.09999.5
2.12-2.233.380.06516.679690.9940.07799.4
2.23-2.373.140.05717.974710.9950.06899
2.37-2.533.570.04822.470580.9970.05799.4
2.53-2.743.510.04225.465780.9970.04999.2
2.74-33.40.03628.860300.9980.04399
3-3.353.10.03130.654190.9980.03898.3
3.35-3.873.470.02736.448240.9980.03299.2
3.87-4.743.50.02538.440670.9990.02999.4
4.74-6.73.160.02536.330930.9980.0398.1
6.7-71.2553.560.02440.317090.9990.02897.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.5→71.255 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 2018 2.49 %in resolution shells
Rwork0.1886 ---
obs0.1892 81007 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.34 Å2 / Biso mean: 34.5866 Å2 / Biso min: 10.9 Å2
Refinement stepCycle: final / Resolution: 1.5→71.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 2 379 3840
Biso mean--38.53 37.28 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043550
X-RAY DIFFRACTIONf_angle_d0.7814811
X-RAY DIFFRACTIONf_chiral_restr0.053545
X-RAY DIFFRACTIONf_plane_restr0.005617
X-RAY DIFFRACTIONf_dihedral_angle_d9.5542123
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2498X-RAY DIFFRACTION7.522TORSIONAL
12B2498X-RAY DIFFRACTION7.522TORSIONAL
13C2498X-RAY DIFFRACTION7.522TORSIONAL
14D2498X-RAY DIFFRACTION7.522TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.53750.291010.309755505651
1.5375-1.57910.31092020.27755355737
1.5791-1.62560.26121010.245756125713
1.6256-1.6780.26432020.221255055707
1.678-1.7380.25981010.202356245725
1.738-1.80760.21321010.190956545755
1.8076-1.88990.21072020.180555515753
1.8899-1.98950.18481010.188756485749
1.9895-2.11420.18942020.179955625764
2.1142-2.27740.20521010.17656575758
2.2774-2.50660.20482010.181456345835
2.5066-2.86940.21291010.189357315832
2.8694-3.61510.22371010.187257765877
3.6151-71.33550.20042010.178559506151
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.18720.2416-0.42911.63420.29421.7385-0.0434-0.05450.01-0.01820.0421-0.012-0.18990.0777-0.00030.173-0.0084-0.0260.1766-0.00190.17826.188747.4452101.0159
20.4646-0.09130.10352.39830.4091.7788-0.0287-0.0629-0.0211-0.0672-0.00750.05110.0371-0.0582-0.00360.0810.0024-0.00120.14170.00310.1569-3.9027-19.470898.3425
31.4774-0.34210.88511.24860.44262.08330.01730.0326-0.119-0.0208-0.01750.07560.071-0.1747-00.134-0.00720.00160.2013-0.00510.1646-2.7726.78383.3553
41.0811-0.153-0.52531.9667-0.91312.3692-0.0052-0.05050.055-0.2679-0.074-0.1635-0.04590.0866-0.01760.2314-0.01210.02270.16120.00210.17257.05962.990282.6921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 119
2X-RAY DIFFRACTION2chain BB2 - 119
3X-RAY DIFFRACTION3chain CC3 - 118
4X-RAY DIFFRACTION4chain DD3 - 118

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