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- PDB-4idl: Low melting temperature Anti-Cholera Toxin Llama VHH domain -

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Basic information

Entry
Database: PDB / ID: 4idl
TitleLow melting temperature Anti-Cholera Toxin Llama VHH domain
ComponentsSingle Domain Antibody VHH A9
KeywordsIMMUNE SYSTEM / v-type immunoglobin fold / Antibody / Cholera Toxin / Single domain Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLegler, P.M. / Lam, A. / Hol, W.G.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of a low-melting-temperature anti-cholera toxin: llama V(H)H domain.
Authors: Legler, P.M. / Zabetakis, D. / Anderson, G.P. / Lam, A. / Hol, W.G. / Goldman, E.R.
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 20, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single Domain Antibody VHH A9


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.444, 51.863, 46.481
Angle α, β, γ (deg.)90.00, 107.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Single Domain Antibody VHH A9


Mass: 14895.435 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VHH domain from Naive Semi-synthetic (Llama) Library, Periplasmic Expression
Source: (gene. exp.) Lama glama (llama) / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.5
Details: Hampton Research Index 8 (0.1 M Sodium Acetate Trihydrate pH 4.5, 3.0 M NaCl), VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 16, 2007
RadiationMonochromator: VariMax HF (Osmic) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→26.87 Å / Num. all: 7796 / Num. obs: 7586 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 20.8
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 5.92 / Num. unique all: 696 / Rsym value: 0.185 / % possible all: 87

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CFI

3cfi


Resolution: 2.09→26.87 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 349 4.6 %RANDOM
Rwork0.20591 ---
obs0.20668 7235 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.895 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.03 Å2
2--0.1 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.09→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 0 59 1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019959
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.9191296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2735122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29123.04346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32715154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8171510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02743
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 21 -
Rwork0.223 482 -
obs--86.72 %

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