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- PDB-5vm0: The hapten triclocarban bound to the single domain camelid nanobo... -

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Basic information

Entry
Database: PDB / ID: 5vm0
TitleThe hapten triclocarban bound to the single domain camelid nanobody VHH T9
ComponentsCamelid Nanobody VHH T9
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: 1.79 Å
AuthorsWogulis, L.A. / Wogulis, M.D. / Tabares-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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Camelid Nanobody VHH T9
B: Camelid Nanobody VHH T9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0467
Polymers27,2292
Non-polymers8175
Water3,765209
1
B: Camelid Nanobody VHH T9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0544
Polymers13,6141
Non-polymers4403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Camelid Nanobody VHH T9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9923
Polymers13,6141
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.113, 52.485, 57.463
Angle α, β, γ (deg.)90.00, 113.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-398-

HOH

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Components

#1: Antibody Camelid Nanobody VHH T9


Mass: 13614.342 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-9EG / N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea / Triclocarban


Mass: 315.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9Cl3N2O / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: protein stock solution was 11 mg/ml well was 10% PEG 3000, 200 mM zinc acetate, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.79→38.47 Å / Num. obs: 25168 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.7
Reflection shellResolution: 1.79→1.88 Å / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 5.2 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OL0

1ol0


Resolution: 1.79→38.47 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.251 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24249 815 3.2 %RANDOM
Rwork0.20425 ---
obs0.20557 24347 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.531 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å2-0.13 Å2
2---1.36 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.79→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 50 209 2137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022002
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9812725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48421.89274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43615314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2691520
X-RAY DIFFRACTIONr_chiral_restr0.1160.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211530
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2981.7051026
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9722.5451284
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1431.978976
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.26315.3133161
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.791→1.837 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 48 -
Rwork0.263 1372 -
obs--74.66 %

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