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- PDB-5vl2: The hapten triclocarban bound to the single domain camelid nanobo... -

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Basic information

Entry
Database: PDB / ID: 5vl2
TitleThe hapten triclocarban bound to the single domain camelid nanobody VHH T4
ComponentsT4 nanobody
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: 1.9 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 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 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 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T4 nanobody
B: T4 nanobody
C: T4 nanobody
D: T4 nanobody
E: T4 nanobody
F: T4 nanobody
G: T4 nanobody
H: T4 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,13216
Polymers113,6078
Non-polymers2,5258
Water3,297183
1
A: T4 nanobody
C: T4 nanobody
F: T4 nanobody
H: T4 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0668
Polymers56,8044
Non-polymers1,2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T4 nanobody
D: T4 nanobody
E: T4 nanobody
G: T4 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0668
Polymers56,8044
Non-polymers1,2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.803, 55.304, 103.426
Angle α, β, γ (deg.)90.00, 111.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
T4 nanobody


Mass: 14200.888 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-9EG / N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea


Mass: 315.582 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H9Cl3N2O / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Drop contained 1 ul 25 mg/ml protein and 2 ul well. Well contained 0.2 M ammonium sulfate, 0.1 M sodium acetate, 30% w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→96.12 Å / Num. obs: 80496 / % possible obs: 98 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 2.2 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→96.12 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU B: 4.896 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26305 4047 5 %RANDOM
Rwork0.21937 ---
obs0.22162 76393 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20.49 Å2
2---0.76 Å20 Å2
3---0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.9→96.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7449 0 152 183 7784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197761
X-RAY DIFFRACTIONr_bond_other_d0.0010.027147
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.95910528
X-RAY DIFFRACTIONr_angle_other_deg0.822316327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40322.105304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.461151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3271572
X-RAY DIFFRACTIONr_chiral_restr0.0950.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219049
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021947
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_it1.9342.5424004
X-RAY DIFFRACTIONr_mcbond_other1.9352.5414003
X-RAY DIFFRACTIONr_mcangle_it2.9693.7954991
X-RAY DIFFRACTIONr_mcangle_other2.9683.7964992
X-RAY DIFFRACTIONr_scbond_it2.4872.8263757
X-RAY DIFFRACTIONr_scbond_other2.4872.8273758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8024.1295538
X-RAY DIFFRACTIONr_long_range_B_refined5.29720.578162
X-RAY DIFFRACTIONr_long_range_B_other5.28920.5638138
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 271 -
Rwork0.397 5548 -
obs--96.56 %

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