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- PDB-5vm6: The hapten triclocarban bound to the single domain camelid nanobo... -

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Basic information

Entry
Database: PDB / ID: 5vm6
TitleThe hapten triclocarban bound to the single domain camelid nanobody VHH T10
Componentssingle domain camelid nanobody VHH T10
KeywordsUNKNOWN FUNCTION / nanobody / triclocarban
Function / homologyN-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTabares-da Rosa, S. / Gonzalez-Sapienza, G. / Wilson, D.K.
CitationJournal: J. Mol. Recognit. / Year: 2019
Title: Structure and specificity of several triclocarban-binding single domain camelid antibody fragments.
Authors: Tabares-da Rosa, S. / Wogulis, L.A. / Wogulis, M.D. / Gonzalez-Sapienza, G. / Wilson, D.K.
History
DepositionApr 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: single domain camelid nanobody VHH T10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9138
Polymers15,0941
Non-polymers8197
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.769, 36.387, 44.598
Angle α, β, γ (deg.)90.00, 111.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody single domain camelid nanobody VHH T10


Mass: 15093.737 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-9EG / N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea


Mass: 315.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9Cl3N2O / Comment: antibiotic*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.84 Å3/Da / Density % sol: 33.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: protein was 21 mg/ml well contained 1.3 M ammonium sulfate, 100 mM citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.5→41.9 Å / Num. obs: 17461 / % possible obs: 98.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.4
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.7 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo T9

Resolution: 1.5→41.59 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.356 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 551 3.2 %RANDOM
Rwork0.17166 ---
obs0.17233 16901 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.333 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20.17 Å2
2---0.61 Å2-0 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.5→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 0 45 99 1133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191060
X-RAY DIFFRACTIONr_bond_other_d0.0020.02934
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9741441
X-RAY DIFFRACTIONr_angle_other_deg0.75532147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.98322.544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89915161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.934159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021204
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02261
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7140.795520
X-RAY DIFFRACTIONr_mcbond_other0.6840.791519
X-RAY DIFFRACTIONr_mcangle_it1.1711.184650
X-RAY DIFFRACTIONr_mcangle_other1.1721.189651
X-RAY DIFFRACTIONr_scbond_it1.3740.965540
X-RAY DIFFRACTIONr_scbond_other1.3310.94525
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0491.345768
X-RAY DIFFRACTIONr_long_range_B_refined3.4947.011212
X-RAY DIFFRACTIONr_long_range_B_other3.3236.7121171
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 31 -
Rwork0.233 1235 -
obs--96.27 %

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