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- PDB-5vm4: The apo form of the triclocarban-binding single domain camelid na... -

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Basic information

Entry
Database: PDB / ID: 5vm4
TitleThe apo form of the triclocarban-binding single domain camelid nanobody VHH T10
ComponentsSingle domain camelid nanobody VHH T10
KeywordsUNKNOWN FUNCTION / nanobody / triclocarban
Function / homologyACETATE ION / FORMIC ACID
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 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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single domain camelid nanobody VHH T10
B: Single domain camelid nanobody VHH T10
C: Single domain camelid nanobody VHH T10
D: Single domain camelid nanobody VHH T10
E: Single domain camelid nanobody VHH T10
F: Single domain camelid nanobody VHH T10
G: Single domain camelid nanobody VHH T10
H: Single domain camelid nanobody VHH T10
I: Single domain camelid nanobody VHH T10
J: Single domain camelid nanobody VHH T10
K: Single domain camelid nanobody VHH T10
L: Single domain camelid nanobody VHH T10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,75524
Polymers181,12512
Non-polymers63012
Water7,927440
1
A: Single domain camelid nanobody VHH T10
B: Single domain camelid nanobody VHH T10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3986
Polymers30,1872
Non-polymers2104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area12960 Å2
MethodPISA
2
F: Single domain camelid nanobody VHH T10
hetero molecules

C: Single domain camelid nanobody VHH T10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2934
Polymers30,1872
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area1610 Å2
ΔGint-13 kcal/mol
Surface area13140 Å2
MethodPISA
3
D: Single domain camelid nanobody VHH T10
I: Single domain camelid nanobody VHH T10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2473
Polymers30,1872
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-12 kcal/mol
Surface area12990 Å2
MethodPISA
4
E: Single domain camelid nanobody VHH T10
J: Single domain camelid nanobody VHH T10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2473
Polymers30,1872
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-13 kcal/mol
Surface area12840 Å2
MethodPISA
5
G: Single domain camelid nanobody VHH T10
hetero molecules

H: Single domain camelid nanobody VHH T10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2804
Polymers30,1872
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area1620 Å2
ΔGint-14 kcal/mol
Surface area12950 Å2
MethodPISA
6
K: Single domain camelid nanobody VHH T10
L: Single domain camelid nanobody VHH T10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2934
Polymers30,1872
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-11 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.566, 93.254, 110.576
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
Single domain camelid nanobody VHH T10


Mass: 15093.737 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein concentration: 21 mg/ml well: 1.8305 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium ...Details: protein concentration: 21 mg/ml well: 1.8305 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, 0.16 M ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: Feb 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→107.26 Å / Num. obs: 120758 / % possible obs: 96.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.3 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T10 holo subunit A

Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.564 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.156 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 6051 5 %RANDOM
Rwork0.19696 ---
obs0.19914 114707 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.835 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20.2 Å2
2---1.27 Å20 Å2
3---2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12144 0 42 440 12626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912498
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211256
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.92116920
X-RAY DIFFRACTIONr_angle_other_deg0.769325872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18851560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14922.34564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.944151944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.06715108
X-RAY DIFFRACTIONr_chiral_restr0.0940.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02114382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023126
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_it1.0611.4766282
X-RAY DIFFRACTIONr_mcbond_other1.0611.4766283
X-RAY DIFFRACTIONr_mcangle_it1.6432.2047824
X-RAY DIFFRACTIONr_mcangle_other1.6432.2047825
X-RAY DIFFRACTIONr_scbond_it1.6221.6566215
X-RAY DIFFRACTIONr_scbond_other1.6231.6566204
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5742.4039097
X-RAY DIFFRACTIONr_long_range_B_refined3.54911.87613706
X-RAY DIFFRACTIONr_long_range_B_other3.54911.87613707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 433 -
Rwork0.236 7983 -
obs--91.83 %

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