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Basic information

Entry
Database: PDB / ID: 6t2j
TitledAb3
ComponentsSingle domain antibody
KeywordsIMMUNE SYSTEM / Human Single Domain Antibody
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTsai, Y.-C.I. / House, D. / Rittinger, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Cell Chem Biol / Year: 2020
Title: Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases.
Authors: Tsai, Y.I. / Johansson, H. / Dixon, D. / Martin, S. / Chung, C.W. / Clarkson, J. / House, D. / Rittinger, K.
History
DepositionOct 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Jan 24, 2024Group: 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single domain antibody
B: Single domain antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2423
Polymers26,1472
Non-polymers951
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-22 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.740, 59.309, 63.846
Angle α, β, γ (deg.)90.000, 131.971, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Single domain antibody


Mass: 13073.577 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium dihydrogen phosphate, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→43.42 Å / Num. obs: 26230 / % possible obs: 99.78 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.07439 / Net I/σ(I): 11.36
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.3836 / Num. unique obs: 2586 / % possible all: 99.35

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PHENIX1.17_3644refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHQ

1ohq


Resolution: 1.7→43.42 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5082
RfactorNum. reflection% reflection
Rfree0.2081 1293 4.93 %
Rwork0.1751 --
obs0.1767 26230 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 5 179 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931876
X-RAY DIFFRACTIONf_angle_d1.03772545
X-RAY DIFFRACTIONf_chiral_restr0.0704270
X-RAY DIFFRACTIONf_plane_restr0.0068323
X-RAY DIFFRACTIONf_dihedral_angle_d8.1527269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.28711410.23332725X-RAY DIFFRACTION99.38
1.77-1.850.28011300.21092766X-RAY DIFFRACTION99.86
1.85-1.950.23991200.1852794X-RAY DIFFRACTION99.66
1.95-2.070.23671610.17312741X-RAY DIFFRACTION99.86
2.07-2.230.21851480.16482751X-RAY DIFFRACTION99.79
2.23-2.450.22691450.16982775X-RAY DIFFRACTION99.9
2.45-2.810.20041600.18042762X-RAY DIFFRACTION99.9
2.81-3.530.18871300.16552798X-RAY DIFFRACTION99.97
3.54-43.420.17291580.16522825X-RAY DIFFRACTION99.77

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