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- PDB-1i3v: THREE-DIMENSIONAL STRUCTURE OF A LAMA VHH DOMAIN UNLIGANDED -

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Basic information

Entry
Database: PDB / ID: 1i3v
TitleTHREE-DIMENSIONAL STRUCTURE OF A LAMA VHH DOMAIN UNLIGANDED
ComponentsANTIBODY VHH LAMA DOMAIN
KeywordsIMMUNE SYSTEM / antibody / domain VHH / Lama
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSpinelli, S. / Tegoni, M. / Frenken, L. / van Vliet, C. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Lateral recognition of a dye hapten by a llama VHH domain.
Authors: Spinelli, S. / Tegoni, M. / Frenken, L. / van Vliet, C. / Cambillau, C.
History
DepositionFeb 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 1.4Oct 30, 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: ANTIBODY VHH LAMA DOMAIN
B: ANTIBODY VHH LAMA DOMAIN


Theoretical massNumber of molelcules
Total (without water)28,0992
Polymers28,0992
Non-polymers00
Water2,630146
1
A: ANTIBODY VHH LAMA DOMAIN


Theoretical massNumber of molelcules
Total (without water)14,0491
Polymers14,0491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANTIBODY VHH LAMA DOMAIN


Theoretical massNumber of molelcules
Total (without water)14,0491
Polymers14,0491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.669, 56.088, 102.365
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody ANTIBODY VHH LAMA DOMAIN


Mass: 14049.452 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG MME 5000, Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal
*PLUS
Density % sol: 42 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16.7 mg/mlprotein1drop
222 %PEG5000 MME1reservoir
30.1 Msodium acetate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→25 Å / Num. all: 57618 / Num. obs: 16273 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.046
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4 / Num. unique all: 2005 / Rsym value: 0.169 / % possible all: 94.6
Reflection
*PLUS
Num. measured all: 57618 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 94.6 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I3U

1i3u


Resolution: 2.03→14.6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1727957.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1066 6.9 %RANDOM
Rwork0.212 ---
obs0.212 15339 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.72 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.63 Å20 Å20 Å2
2--3.18 Å20 Å2
3---0.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.03→14.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 0 147 2121
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d28
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 174 7 %
Rwork0.272 2328 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 0 / Rfactor obs: 0.211 / Rfactor Rfree: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.345 / % reflection Rfree: 7 % / Rfactor Rwork: 0.272

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