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- PDB-6qb2: Crystal structure of the cystatin-based engineered protein scaffo... -

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Basic information

Entry
Database: PDB / ID: 6qb2
TitleCrystal structure of the cystatin-based engineered protein scaffold SQT-1C
ComponentsMonomer of SQT-1C
KeywordsDE NOVO PROTEIN / Engineered Scaffold protein
Function / homologyNuclear Transport Factor 2; Chain: A, - #10 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Union675074 United Kingdom
CitationJournal: Sci Rep / Year: 2019
Title: Studies of the oligomerisation mechanism of a cystatin-based engineered protein scaffold.
Authors: Zalar, M. / Indrakumar, S. / Levy, C.W. / Tunnicliffe, R.B. / Peters, G.H.J. / Golovanov, A.P.
History
DepositionDec 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.pdbx_keywords

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monomer of SQT-1C


Theoretical massNumber of molelcules
Total (without water)15,3211
Polymers15,3211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.124, 96.124, 29.859
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Monomer of SQT-1C


Mass: 15321.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 38% Dioxane / Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→42.99 Å / Num. obs: 5209 / % possible obs: 99.79 % / Redundancy: 11.9 % / Biso Wilson estimate: 84.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.018 / Rrim(I) all: 0.061 / Net I/σ(I): 17.39
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 497 / CC1/2: 0.685 / Rpim(I) all: 0.27 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K9M

3k9m


Resolution: 2.5→42.99 Å / SU ML: 0.3765 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 28.5026
RfactorNum. reflection% reflection
Rfree0.2948 256 4.92 %
Rwork0.275 --
obs0.276 5207 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 106.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms756 0 0 0 756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023767
X-RAY DIFFRACTIONf_angle_d0.57491034
X-RAY DIFFRACTIONf_chiral_restr0.0442116
X-RAY DIFFRACTIONf_plane_restr0.0048133
X-RAY DIFFRACTIONf_dihedral_angle_d14.9219470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-3.150.42441260.3262398X-RAY DIFFRACTION99.72
3.15-42.990.27671300.26712553X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 46.0228387245 Å / Origin y: 21.4256424397 Å / Origin z: 0.780314274909 Å
111213212223313233
T0.633970684832 Å20.0256486061824 Å2-0.0705882056698 Å2-0.759094912975 Å2-0.146931050128 Å2--0.902499162213 Å2
L7.23135243632 °21.16376806008 °2-0.666811463347 °2-8.28102122268 °2-2.5741415421 °2--3.61991145211 °2
S0.28070581197 Å °0.253232878746 Å °0.869863050378 Å °-0.52751959938 Å °-0.354867644363 Å °-0.0433073567628 Å °0.630889176777 Å °-0.0846273668361 Å °-0.0299299044925 Å °
Refinement TLS groupSelection details: all

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