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- PDB-5nml: Nb36 Ser85Cys with Hg bound -

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Basic information

Entry
Database: PDB / ID: 5nml
TitleNb36 Ser85Cys with Hg bound
ComponentsNanobody Nb36 Ser85Cys
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: 2.5 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 6, 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 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Nanobody Nb36 Ser85Cys
B: Nanobody Nb36 Ser85Cys
C: Nanobody Nb36 Ser85Cys
D: Nanobody Nb36 Ser85Cys
E: Nanobody Nb36 Ser85Cys
F: Nanobody Nb36 Ser85Cys
G: Nanobody Nb36 Ser85Cys
H: Nanobody Nb36 Ser85Cys
I: Nanobody Nb36 Ser85Cys
J: Nanobody Nb36 Ser85Cys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,99623
Polymers135,94310
Non-polymers2,05413
Water0
1
A: Nanobody Nb36 Ser85Cys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7952
Polymers13,5941
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nanobody Nb36 Ser85Cys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0584
Polymers13,5941
Non-polymers4633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nanobody Nb36 Ser85Cys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0584
Polymers13,5941
Non-polymers4633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nanobody Nb36 Ser85Cys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9953
Polymers13,5941
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nanobody Nb36 Ser85Cys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6562
Polymers13,5941
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nanobody Nb36 Ser85Cys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7952
Polymers13,5941
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Nanobody Nb36 Ser85Cys


Theoretical massNumber of molelcules
Total (without water)13,5941
Polymers13,5941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Nanobody Nb36 Ser85Cys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8573
Polymers13,5941
Non-polymers2632
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Nanobody Nb36 Ser85Cys


Theoretical massNumber of molelcules
Total (without water)13,5941
Polymers13,5941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Nanobody Nb36 Ser85Cys


Theoretical massNumber of molelcules
Total (without water)13,5941
Polymers13,5941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.960, 99.110, 85.410
Angle α, β, γ (deg.)90.000, 105.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))
21(chain B and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))
31(chain C and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))
41(chain D and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))
51(chain E and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))
61(chain F and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))
71(chain G and (resid 3 through 84 or resid 86 through 118))
81(chain H and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))
91(chain I and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))

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
11VALVALASNASN(chain A and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))AA3 - 843 - 84
12LEULEUALAALA(chain A and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))AA86 - 10186 - 101
13TRPTRPSERSER(chain A and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))AA109 - 118109 - 118
21VALVALASNASN(chain B and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))BB3 - 843 - 84
22LEULEUALAALA(chain B and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))BB86 - 10186 - 101
23TRPTRPSERSER(chain B and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))BB109 - 118109 - 118
31VALVALASNASN(chain C and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))CC3 - 843 - 84
32LEULEUALAALA(chain C and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))CC86 - 10186 - 101
33TRPTRPSERSER(chain C and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))CC109 - 118109 - 118
41VALVALASNASN(chain D and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))DD3 - 843 - 84
42LEULEUALAALA(chain D and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))DD86 - 10186 - 101
43TRPTRPSERSER(chain D and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))DD109 - 118109 - 118
51VALVALASNASN(chain E and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))EE3 - 843 - 84
52LEULEUALAALA(chain E and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))EE86 - 10186 - 101
53TRPTRPSERSER(chain E and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))EE109 - 118109 - 118
61VALVALASNASN(chain F and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))FF3 - 843 - 84
62LEULEUALAALA(chain F and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))FF86 - 10186 - 101
63TRPTRPSERSER(chain F and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))FF109 - 118109 - 118
71VALVALASNASN(chain G and (resid 3 through 84 or resid 86 through 118))GG3 - 843 - 84
72LEULEUSERSER(chain G and (resid 3 through 84 or resid 86 through 118))GG86 - 11886 - 118
81VALVALASNASN(chain H and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))HH3 - 843 - 84
82LEULEUALAALA(chain H and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))HH86 - 10186 - 101
83TRPTRPSERSER(chain H and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))HH109 - 118109 - 118
91VALVALASNASN(chain I and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))II3 - 843 - 84
92LEULEUALAALA(chain I and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))II86 - 10186 - 101
93TRPTRPSERSER(chain I and (resid 3 through 84 or resid 86 through 101 or resid 109 through 118))II109 - 118109 - 118

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Components

#1: Antibody
Nanobody Nb36 Ser85Cys


Mass: 13594.275 Da / Num. of mol.: 10
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 / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2

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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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M NaMalonate pH 7, 20% 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: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.5→45.415 Å / Num. obs: 85113 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 3.151 % / Biso Wilson estimate: 67.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.087 / Χ2: 1.44 / Net I/σ(I): 10.35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.5621.2760.5740870.1571.72260.8
2.56-2.642.0851.1710.6947640.1991.56271.6
2.64-2.712.1780.9130.952730.3511.19782
2.71-2.82.4350.7231.2257410.5010.9291.7
2.8-2.892.9420.6231.6659050.6410.76197.6
2.89-2.993.5540.5032.4458320.7860.59399.6
2.99-3.13.5870.3613.4656690.8830.42599.5
3.1-3.233.540.2614.5953760.9270.30999.6
3.23-3.373.3220.1686.5552030.9660.20199.5
3.37-3.543.5360.1259.1349890.9830.14899.6
3.54-3.733.5860.0921247150.990.10999.9
3.73-3.953.5110.07115.1344710.9930.08499.8
3.95-4.233.2970.05418.2942320.9950.06499.6
4.23-4.563.6070.04324.0638460.9970.0599.8
4.56-53.5530.04125.0836430.9970.04899.6
5-5.593.3290.04124.4832270.9970.04999.5
5.59-6.463.5720.04425.3228900.9970.05299.6
6.46-7.913.4030.03729.4923870.9970.04499.2
7.91-11.183.4020.02736.6718460.9990.03298.6
11.18-45.4153.3330.02439.1810170.9990.02997.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.415 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.98
RfactorNum. reflection% reflection
Rfree0.2646 2014 4.61 %
Rwork0.238 --
obs0.2392 43705 93.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 217.37 Å2 / Biso mean: 86.8523 Å2 / Biso min: 36.51 Å2
Refinement stepCycle: final / Resolution: 2.5→45.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8462 0 25 0 8487
Biso mean--84.95 --
Num. residues----1128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028619
X-RAY DIFFRACTIONf_angle_d0.65811639
X-RAY DIFFRACTIONf_chiral_restr0.0451311
X-RAY DIFFRACTIONf_plane_restr0.0031489
X-RAY DIFFRACTIONf_dihedral_angle_d8.7365107
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4496X-RAY DIFFRACTION11.17TORSIONAL
12B4496X-RAY DIFFRACTION11.17TORSIONAL
13C4496X-RAY DIFFRACTION11.17TORSIONAL
14D4496X-RAY DIFFRACTION11.17TORSIONAL
15E4496X-RAY DIFFRACTION11.17TORSIONAL
16F4496X-RAY DIFFRACTION11.17TORSIONAL
17G4496X-RAY DIFFRACTION11.17TORSIONAL
18H4496X-RAY DIFFRACTION11.17TORSIONAL
19I4496X-RAY DIFFRACTION11.17TORSIONAL
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 (%)
2.4999-2.56240.3603950.39671976207162
2.5624-2.63170.3611150.37542309242473
2.6317-2.70910.40161320.35892645277784
2.7091-2.79660.33361420.33192936307893
2.7966-2.89650.39471470.32193113326098
2.8965-3.01250.34651590.307431783337100
3.0125-3.14950.31141550.304931543309100
3.1495-3.31550.28591490.278731873336100
3.3155-3.52320.26171480.259131953343100
3.5232-3.79510.27541590.243131603319100
3.7951-4.17680.27721460.228131853331100
4.1768-4.78060.2111510.182431963347100
4.7806-6.02080.21241600.204332053365100
6.0208-45.4220.24321560.209532523408100
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)
14.572.3808-0.94826.893-1.73725.3936-0.01370.01260.0530.01780.03910.0246-0.0277-0.00490.06320.2220.0416-0.03030.34070.03220.315457.009919.583261.3607
25.4569-0.678-0.07835.29210.46925.5602-0.08010.33850.153-0.16420.34110.2324-0.2037-0.359-0.23050.2880.00050.02660.49530.17930.477833.423214.109968.5031
34.3281-2.134-0.07346.95330.03644.962-0.1991-0.3252-0.03260.51850.0948-0.1110.36780.05120.02590.39920.07510.0190.3927-0.00580.350775.675514.516980.9733
43.82651.7815-1.54917.5036-4.79186.454-0.09570.1819-0.0476-0.2760.41510.29640.3991-0.4797-0.25760.58610.01850.01640.36540.02970.40745.2827-12.428671.7136
56.1048-1.25741.18176.5318-0.93517.3669-0.02230.3162-0.1918-0.33450.1274-0.44730.44550.7038-0.02210.46130.1654-0.04640.5257-0.11820.566412.18683.002660.8981
64.0161-0.6209-0.22948.29293.23524.85210.1606-0.26230.13240.126-0.21810.4319-0.5725-0.13150.07060.51960.0515-0.03670.4688-0.16170.473282.84420.337639.7039
74.39280.93882.40675.17042.83616.3418-0.33060.7687-0.0297-0.75440.12590.34-0.3583-1.89630.19670.8129-0.0355-0.05991.43020.14540.453241.4520.325937.1002
84.8016-0.50211.17158.3194-3.74134.98710.15190.26630.2790.123-0.10160.159-0.3447-0.13370.13550.81910.08730.06130.49920.07810.512554.9836-18.537525.3836
95.6139-0.0081-0.3687.3961-1.31428.55640.32120.04360.19240.424-0.3852-0.5018-0.07590.7272-0.00770.7342-0.0150.07660.58620.12050.565459.90474.201415.2779
103.75061.5722.90016.0862-1.02894.1684-0.58331.1588-0.59740.1180.2434-0.1523-0.27520.91190.43030.787-0.07170.07241.7251-0.32580.851723.0115-0.127529.062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 120
2X-RAY DIFFRACTION2chain BB2 - 119
3X-RAY DIFFRACTION3chain CC2 - 119
4X-RAY DIFFRACTION4chain DD3 - 119
5X-RAY DIFFRACTION5chain EE2 - 119
6X-RAY DIFFRACTION6chain FF2 - 119
7X-RAY DIFFRACTION7chain GG3 - 119
8X-RAY DIFFRACTION8chain HH3 - 119
9X-RAY DIFFRACTION9chain II2 - 118
10X-RAY DIFFRACTION10chain JJ10 - 119

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