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- PDB-5h8d: Crystal structure of an ASC binding nanobody -

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Basic information

Entry
Database: PDB / ID: 5h8d
TitleCrystal structure of an ASC binding nanobody
ComponentsVHH nanobody
KeywordsIMMUNE SYSTEM / VHH nanobody / ASC-binding / antibody fragment / inflammasome
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsLu, A. / Schmidt, F.I. / Ruan, J. / Tang, C. / Wu, H. / Ploegh, H.L.
CitationJournal: J.Exp.Med. / Year: 2016
Title: A single domain antibody fragment that recognizes the adaptor ASC defines the role of ASC domains in inflammasome assembly.
Authors: Schmidt, F.I. / Lu, A. / Chen, J.W. / Ruan, J. / Tang, C. / Wu, H. / Ploegh, H.L.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VHH nanobody


Theoretical massNumber of molelcules
Total (without water)12,2541
Polymers12,2541
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.421, 97.421, 31.881
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

21A-318-

HOH

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Components

#1: Antibody VHH nanobody


Mass: 12253.590 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1 M citric acid at pH 3.5 and 35% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→68.89 Å / Num. obs: 12777 / % possible obs: 99.2 % / Redundancy: 9.7 % / Net I/σ(I): 8.77

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.89 Å68.89 Å
Translation1.89 Å68.89 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
HKL-2000data reduction
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→68.89 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 18.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 1274 10 %
Rwork0.1687 11461 -
obs0.1721 12735 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.79 Å2 / Biso mean: 28.1668 Å2 / Biso min: 11.46 Å2
Refinement stepCycle: final / Resolution: 1.89→68.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 0 127 988
Biso mean---37.42 -
Num. residues----114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006880
X-RAY DIFFRACTIONf_angle_d0.9671185
X-RAY DIFFRACTIONf_chiral_restr0.047122
X-RAY DIFFRACTIONf_plane_restr0.004154
X-RAY DIFFRACTIONf_dihedral_angle_d12.821313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.96510.20561300.16821176130694
1.9651-2.05460.19631380.16281234137299
2.0546-2.16290.23871400.169812651405100
2.1629-2.29840.21341400.165412611401100
2.2984-2.47590.21351410.182912661407100
2.4759-2.7250.25641400.184612621402100
2.725-3.11940.24631440.193112891433100
3.1194-3.930.17651460.167213131459100
3.93-68.93280.16881550.14913951550100
Refinement TLS params.Method: refined / Origin x: -29.2134 Å / Origin y: 10.7299 Å / Origin z: 4.443 Å
111213212223313233
T0.1251 Å2-0.0006 Å20.0191 Å2-0.1482 Å20.026 Å2--0.1205 Å2
L2.0139 °2-0.6631 °2-0.1559 °2-4.4696 °21.2971 °2--1.7168 °2
S0.1071 Å °0.1668 Å °0.0199 Å °-0.0628 Å °-0.1528 Å °-0.0908 Å °0.0238 Å °-0.1324 Å °0.0306 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 116
2X-RAY DIFFRACTION1allS1 - 128

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