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- PDB-1sjx: Three-Dimensional Structure of a Llama VHH Domain OE7 binding the... -

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Basic information

Entry
Database: PDB / ID: 1sjx
TitleThree-Dimensional Structure of a Llama VHH Domain OE7 binding the cell wall protein Malf1
Componentsimmunoglobulin VH domain
KeywordsIMMUNE SYSTEM / Camelids antibody / heavy chain / dandruff / phage display
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDolk, E. / van der Vaart, M. / Hulsik, D.L. / Vriend, G. / de Haard, H. / Spinelli, S. / Cambillau, C. / Frenken, L. / Verrips, T.
CitationJournal: Appl.Environ.Microbiol. / Year: 2005
Title: Isolation of llama antibody fragments for prevention of dandruff by phage display in shampoo.
Authors: Dolk, E. / van der Vaart, M. / Hulsik, D.L. / Vriend, G. / de Haard, H. / Spinelli, S. / Cambillau, C. / Frenken, L. / Verrips, T.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence of the protein was not deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: immunoglobulin VH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4513
Polymers13,2151
Non-polymers2362
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.40, 71.40, 74.84
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody immunoglobulin VH domain


Mass: 13214.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Description: Protein selected by phage display / Cell: lymphocytes / Production host: Saccharomyces cerevisiae (brewer's yeast)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 4.17 Å3/Da / Density % sol: 70.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 10% PEG 6K, 100mM Hepes, 5% MPD, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 2.2→24 Å / Num. obs: 11594 / % possible obs: 99.8 % / Observed criterion σ(F): 3.5 / Observed criterion σ(I): 3.5 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 3.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1637 / Rsym value: 0.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HCV

1hcv


Resolution: 2.2→24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.613 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.165 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20644 804 7 %RANDOM
Rwork0.19054 ---
all0.2 10773 --
obs0.19163 10763 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.713 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 16 86 1002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021929
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9491256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5085118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02699
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2337
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.217
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5361.5581
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0492923
X-RAY DIFFRACTIONr_scbond_it1.563348
X-RAY DIFFRACTIONr_scangle_it2.5614.5333
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 50
Rwork0.234 782
Refinement TLS params.Method: refined / Origin x: -2.283 Å / Origin y: 49.94 Å / Origin z: 5.464 Å
111213212223313233
T0.0713 Å2-0.0425 Å2-0.0115 Å2-0.0298 Å2-0.0134 Å2--0.0922 Å2
L0.9916 °20.3846 °20.5605 °2-5.4586 °20.3317 °2--1.5962 °2
S-0.0387 Å °0.0877 Å °-0.0658 Å °-0.2648 Å °0.1868 Å °-0.036 Å °0.0915 Å °-0.0609 Å °-0.1481 Å °

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