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- PDB-1u0q: Structure of a Llama VHH domain raised against a carbazole molecule -

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Basic information

Entry
Database: PDB / ID: 1u0q
TitleStructure of a Llama VHH domain raised against a carbazole molecule
Componentsimmunoglobulin heavy chain variable domain
KeywordsIMMUNE SYSTEM / immunoglobulin domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCambillau, C. / Spinelli, S. / Desmyter, A. / Verrips, T.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a Llama VHH Domain Raised Against a Carbazole Hapten
Authors: Cambillau, C. / Spinelli, S. / Desmyter, A. / Verrips, T.
History
DepositionJul 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: immunoglobulin heavy chain variable domain
B: immunoglobulin heavy chain variable domain


Theoretical massNumber of molelcules
Total (without water)27,3802
Polymers27,3802
Non-polymers00
Water4,378243
1
A: immunoglobulin heavy chain variable domain


Theoretical massNumber of molelcules
Total (without water)13,6901
Polymers13,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: immunoglobulin heavy chain variable domain


Theoretical massNumber of molelcules
Total (without water)13,6901
Polymers13,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.235, 48.235, 163.983
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody immunoglobulin heavy chain variable domain


Mass: 13690.122 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Saccharomyces cerevisiae (brewer's yeast)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 5000 30%, AmSO4 200mM, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.988 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2001 / Details: miror
RadiationMonochromator: miror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.6→29 Å / Num. all: 28590 / Num. obs: 28590 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 8.3
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 6.3 / % possible all: 63

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 1330 RANDOM
Rwork0.221 --
obs0.221 27290 -
all-27290 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.621 Å2-0.504 Å20 Å2
2--0.621 Å20 Å2
3----1.243 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 0 243 2161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.27
LS refinement shellResolution: 1.6→1.7 Å /
RfactorNum. reflection
Rfree0.31 135
Rwork0.29 -
obs-2713
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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