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- PDB-5vlv: The apo form of the triclocarban-binding single domain camelid na... -

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Basic information

Entry
Database: PDB / ID: 5vlv
TitleThe apo form of the triclocarban-binding single domain camelid nanobody VHH T9
ComponentsSingle Domain Camelid Nanobody VHH T9
KeywordsUNKNOWN FUNCTION / nanobody / triclocarban
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Single Domain Camelid Nanobody VHH T9


Theoretical massNumber of molelcules
Total (without water)14,2891
Polymers14,2891
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.814, 48.814, 119.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

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Components

#1: Antibody Single Domain Camelid Nanobody VHH T9


Mass: 14289.056 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein concentration 40 mg/ml well 25% w/v PEG MME 3350, 200 mM ammonium sulfate, 100 mM Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CCD / Date: Jan 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.35→48.81 Å / Num. obs: 32653 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 24.5
Reflection shellResolution: 1.35→1.39 Å / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T9 holo

Resolution: 1.35→48.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.472 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18887 1622 5 %RANDOM
Rwork0.16177 ---
obs0.16314 30970 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.35→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 0 70 1003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02957
X-RAY DIFFRACTIONr_bond_other_d0.0010.02900
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9541299
X-RAY DIFFRACTIONr_angle_other_deg0.74532065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.83321.89237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.67915153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0821510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
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_it2.1042.115504
X-RAY DIFFRACTIONr_mcbond_other2.0462.11503
X-RAY DIFFRACTIONr_mcangle_it2.7053.177630
X-RAY DIFFRACTIONr_mcangle_other2.7063.181631
X-RAY DIFFRACTIONr_scbond_it4.472.713453
X-RAY DIFFRACTIONr_scbond_other4.4742.712453
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0953.827670
X-RAY DIFFRACTIONr_long_range_B_refined4.3517.8491009
X-RAY DIFFRACTIONr_long_range_B_other4.33117.7561001
X-RAY DIFFRACTIONr_rigid_bond_restr2.61631857
X-RAY DIFFRACTIONr_sphericity_free23.137542
X-RAY DIFFRACTIONr_sphericity_bonded12.6851867
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 98 -
Rwork0.224 2264 -
obs--99.83 %

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