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- PDB-6f0d: Crystal structure of a llama VHH antibody BCD090-M2 against human... -

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Entry
Database: PDB / ID: 6f0d
TitleCrystal structure of a llama VHH antibody BCD090-M2 against human ErbB3 in space group P1 with cadmium ions
ComponentsVHH antibody BCD090-M2
KeywordsIMMUNE SYSTEM / VHH / llama antibody / single-domain antibody / nanobody / ErbB3 / Her3 / receptor tyrosine kinase
Function / homology:
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.90000753152 Å
AuthorsEliseev, I.E. / Yudenko, A.N. / Vysochinskaya, V.V. / Svirina, A.A. / Evstratyeva, A.V. / Drozhzhachih, M.S. / Krendeleva, E.A. / Vladimirova, A.K. / Nemankin, T.A. / Ekimova, V.M. ...Eliseev, I.E. / Yudenko, A.N. / Vysochinskaya, V.V. / Svirina, A.A. / Evstratyeva, A.V. / Drozhzhachih, M.S. / Krendeleva, E.A. / Vladimirova, A.K. / Nemankin, T.A. / Ekimova, V.M. / Ulitin, A.B. / Lomovskaya, M.I. / Yakovlev, P.A. / Moiseenko, F.V. / Chakchir, O.B.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Education and ScienceRFMEFI57716X0217 Russian Federation
CitationJournal: F1000Res / Year: 2018
Title: Crystal structures of a llama VHH antibody BCD090-M2 targeting human ErbB3 receptor.
Authors: Eliseev, I.E. / Yudenko, A.N. / Vysochinskaya, V.V. / Svirina, A.A. / Evstratyeva, A.V. / Drozhzhachih, M.S. / Krendeleva, E.A. / Vladimirova, A.K. / Nemankin, T.A. / Ekimova, V.M. / Ulitin, ...Authors: Eliseev, I.E. / Yudenko, A.N. / Vysochinskaya, V.V. / Svirina, A.A. / Evstratyeva, A.V. / Drozhzhachih, M.S. / Krendeleva, E.A. / Vladimirova, A.K. / Nemankin, T.A. / Ekimova, V.M. / Ulitin, A.B. / Lomovskaya, M.I. / Yakovlev, P.A. / Bukatin, A.S. / Knyazev, N.A. / Moiseenko, F.V. / Chakchir, O.B.
History
DepositionNov 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: VHH antibody BCD090-M2
A: VHH antibody BCD090-M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1604
Polymers27,9352
Non-polymers2252
Water2,792155
1
B: VHH antibody BCD090-M2


Theoretical massNumber of molelcules
Total (without water)13,9671
Polymers13,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: VHH antibody BCD090-M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1923
Polymers13,9671
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.766, 41.526, 46.487
Angle α, β, γ (deg.)89.992, 67.921, 76.062
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody VHH antibody BCD090-M2


Mass: 13967.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 17 mg/ml in 20 mM HEPES pH 7.5, 50 mM NaCl Reservoir solution: 0.1 M MES pH 6.5, 12% w/v PEG 3350, 5 mM CdSO4

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Data collection

DiffractionMean temperature: 293.15 K
Ambient temp details: Room temperature data collection in a sealed quartz capillary tube
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54184 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.90000753152→32.3416437838 Å / Num. obs: 18859 / % possible obs: 100 % / Redundancy: 13.0920515404 % / Biso Wilson estimate: 15.2376005709 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.144282201545 / Rpim(I) all: 0.0395 / Rrim(I) all: 0.15 / Net I/σ(I): 12.9301230207
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID
5.15080833411-32.346314013120.0171673820.073619492476346.92361547139321
4.09095425893-5.1508083341120.59770114940.075466775903947.82354113549571
3.57458139652-4.0909542589320.47216274090.098182148064738.79228207969341
3.24808807264-3.5745813965218.71762208070.11760753955930.88752321869421
3.01546142965-3.2480880726417.47639034630.14565953668123.82133772459531
2.83778558507-3.0154614296516.91693290730.19213821380917.29843098769391
2.69573965383-2.8377855850716.52990556140.21671300264414.90920604549531
2.57844441163-2.6957396538316.73729729730.24787489916513.33449054839251
2.47922007445-2.5784444116315.85088633990.28653215514110.82267958659591
2.39369659134-2.4792200744515.36836518050.31274330386510.17607884659421
2.31887251552-2.3936965913413.60021208910.3624895122547.846160872249431
2.25260545186-2.3188725155211.96529968450.3866092803887.023047328359511
2.19331759784-2.2526054518610.47983014860.3936596240866.181689803449421
2.13981643674-2.193317597849.446921443740.4432158436585.258552337599421
2.0911807483-2.139816436748.19176598050.5110577402814.096708631419231
2.04668548244-2.09118074837.070466321240.5513419964273.486906225939651
2.00575070422-2.046685482446.364705882350.6013925370082.911024807429351
1.96790596897-2.005750704225.80683030950.6551033195542.521144571529371
1.93276488574-1.967905968975.360416666670.7824349126191.800643322189601
1.90000753152-1.932764885744.791351351350.8333872062631.564741696359251

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Processing

Software
NameVersionClassification
APEX 22014.11-0data collection
SAINTV8.18Cdata reduction
SADABS2008/1data scaling
PHASER2.7.16phasing
PHENIX1.11.1_2575model building
Coot0.8.6.1model building
PHENIX1.11.1_2575refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EZW

6ezw


Resolution: 1.90000753152→32.3416437838 Å / SU ML: 0.2149427553 / Cross valid method: FREE R-VALUE / σ(F): 0.119369942261 / Phase error: 22.3042350655
RfactorNum. reflection% reflection
Rfree0.217608275476 1829 10.023016221 %
Rwork0.17376345673 --
obs0.178155788177 18248 96.765298547 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.8620885272 Å2
Refinement stepCycle: LAST / Resolution: 1.90000753152→32.3416437838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 2 155 2119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01391470742032006
X-RAY DIFFRACTIONf_angle_d1.530855361852714
X-RAY DIFFRACTIONf_chiral_restr0.072200302117280
X-RAY DIFFRACTIONf_plane_restr0.0082941237946358
X-RAY DIFFRACTIONf_dihedral_angle_d20.0180771652722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.3136031984281360.2573796532681202X-RAY DIFFRACTION91.9587628866
1.9514-2.00880.3003728494561350.2385550248621201X-RAY DIFFRACTION93.2960893855
2.0088-2.07360.233652896661410.2211785605341267X-RAY DIFFRACTION95.3283683142
2.0736-2.14770.245518931011360.1951863130131213X-RAY DIFFRACTION95
2.1477-2.23370.2418804567221440.1881344661791265X-RAY DIFFRACTION95.460704607
2.2337-2.33530.2204472903941380.1849194955051242X-RAY DIFFRACTION96.2343096234
2.3353-2.45840.2650870814811410.1913013761011283X-RAY DIFFRACTION97.4674880219
2.4584-2.61240.2203325420391390.1875101911731277X-RAY DIFFRACTION98.0609418283
2.6124-2.8140.2427163070021410.1788498945271281X-RAY DIFFRACTION98.4764542936
2.814-3.09690.2210612131641430.1776553366491291X-RAY DIFFRACTION98.5567010309
3.0969-3.54460.2018728100511460.1642785077231298X-RAY DIFFRACTION98.904109589
3.5446-4.46390.1786955891181440.1390908123371296X-RAY DIFFRACTION99.6539792388
4.4639-32.34630.1686279524331450.1301908391451303X-RAY DIFFRACTION99.7932460372

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