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- PDB-1i3u: THREE-DIMENSIONAL STRUCTURE OF A LLAMA VHH DOMAIN COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1i3u
TitleTHREE-DIMENSIONAL STRUCTURE OF A LLAMA VHH DOMAIN COMPLEXED WITH THE DYE RR1
ComponentsANTIBODY VHH LAMA DOMAIN
KeywordsIMMUNE SYSTEM / antibody / VHH fragment / Lama glama
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-RR1
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AN APPROPRIATE SEQUENCE DATABASE MATCH WAS NOT AVAILABLE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIBODY VHH LAMA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5513
Polymers13,8421
Non-polymers7092
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.435, 77.435, 175.019
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Antibody ANTIBODY VHH LAMA DOMAIN


Mass: 13842.268 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RR1 / 5-(4,6-DIAMINO-[1,3,5]TRIAZIN-2-YLAMINO)-4-HYDROXY-3-(2-SULFO-PHENYLAZO)-NAPHTHALENE-2,7-DISULFONIC ACID / REACTIVE RED 1 DYE


Mass: 612.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16N8O10S3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.65 Å3/Da / Density % sol: 66.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MME 5000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
20.9-1.8 Mammonium sulfate1reservoir
30.1 MHEPES1reservoirpH7.5
41 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.988 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 189080 / Num. obs: 15022 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.057 / Net I/σ(I): 4.7
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 1088 / Rsym value: 0.144 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 189080 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.144

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VHH52 anti-R1 unliganded

Resolution: 1.95→18.5 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2310814.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1194 8 %RANDOM
Rwork0.232 ---
obs0.232 15003 99.3 %-
all-0 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.87 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.94 Å25.75 Å20 Å2
2--5.94 Å20 Å2
3----11.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.95→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 45 164 1186
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.382.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 133 9.2 %
Rwork0.29 1319 -
obs-0 54.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3RR1_240399.PARAMRR1_240399.TOP
X-RAY DIFFRACTION4SO4.PARAMSO4.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
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: 0.305 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.29

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