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- PDB-6i37: Crystal structure of nv1Pizza6-AYW, a circularly permuted designe... -

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Basic information

Entry
Database: PDB / ID: 6i37
TitleCrystal structure of nv1Pizza6-AYW, a circularly permuted designer protein
Componentsnv1Pizza6-AYW
KeywordsDE NOVO PROTEIN / circularly permuted designer protein / artificial protein / beta-propeller / Pizza
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsMylemans, B. / Noguchi, H. / Deridder, E. / Voet, A.R.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - FlandersG0F9316N Belgium
Research Foundation - FlandersG051917N Belgium
Research Foundation - FlandersGBM-D3229-ASP/17 Belgium
CitationJournal: Protein Sci. / Year: 2020
Title: Influence of circular permutations on the structure and stability of a six-fold circular symmetric designer protein.
Authors: Mylemans, B. / Noguchi, H. / Deridder, E. / Lescrinier, E. / Tame, J.R.H. / Voet, A.R.D.
History
DepositionNov 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nv1Pizza6-AYW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1455
Polymers25,7601
Non-polymers3844
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-31 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.256, 55.977, 69.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein nv1Pizza6-AYW


Mass: 25760.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PET28b / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 1.82 Å3/Da / Density % sol: 32.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.6M Ammonium sulfate + 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.54→43.559 Å / Num. obs: 27927 / % possible obs: 98.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/σ(I): 17.6
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 1288 / Rpim(I) all: 0.085 / Rrim(I) all: 0.162 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F0Q

6f0q


Resolution: 1.54→43.559 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 21.67
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1446 5.18 %Random selection
Rwork0.1895 ---
obs0.1912 27896 98.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.54→43.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 20 302 2110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072009
X-RAY DIFFRACTIONf_angle_d0.8722810
X-RAY DIFFRACTIONf_dihedral_angle_d2.7581460
X-RAY DIFFRACTIONf_chiral_restr0.057354
X-RAY DIFFRACTIONf_plane_restr0.006373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.5950.27871400.21132450X-RAY DIFFRACTION94
1.595-1.65890.27791390.20782573X-RAY DIFFRACTION97
1.6589-1.73440.26961550.19792589X-RAY DIFFRACTION98
1.7344-1.82590.22811380.20372627X-RAY DIFFRACTION98
1.8259-1.94030.25011380.19392639X-RAY DIFFRACTION98
1.9403-2.09010.22241450.18312628X-RAY DIFFRACTION99
2.0901-2.30040.25751500.18922679X-RAY DIFFRACTION99
2.3004-2.63320.21741490.19372672X-RAY DIFFRACTION99
2.6332-3.31740.22981410.19072731X-RAY DIFFRACTION100
3.3174-43.57590.18821510.18052862X-RAY DIFFRACTION99

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