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- PDB-6i3b: Crystal structure of cPizza6-AYW, a circularly permuted designer ... -

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Basic information

Entry
Database: PDB / ID: 6i3b
TitleCrystal structure of cPizza6-AYW, a circularly permuted designer protein
ComponentscPizza6-AYW
KeywordsDE NOVO PROTEIN / circularly permuted designer protein / artificial protein / beta-propeller / Pizza
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 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 1.2May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: cPizza6-AYW
B: cPizza6-AYW


Theoretical massNumber of molelcules
Total (without water)50,8882
Polymers50,8882
Non-polymers00
Water13,295738
1
A: cPizza6-AYW


Theoretical massNumber of molelcules
Total (without water)25,4441
Polymers25,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cPizza6-AYW


Theoretical massNumber of molelcules
Total (without water)25,4441
Polymers25,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.051, 70.442, 58.144
Angle α, β, γ (deg.)90.00, 100.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein cPizza6-AYW


Mass: 25444.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 1.86 Å3/Da / Density % sol: 33.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.25M Sodium chloride 0.1M HEPES pH7 25%(w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.75 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1→46.26 Å / Num. obs: 200513 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Net I/σ(I): 14.4
Reflection shellResolution: 1→1.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.208 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 9930 / CC1/2: 0.704 / Rpim(I) all: 0.512 / Rrim(I) all: 1.314 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1→39.675 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.52
RfactorNum. reflection% reflection
Rfree0.1748 9891 4.94 %
Rwork0.153 --
obs0.1541 200404 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1→39.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 0 738 4326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093940
X-RAY DIFFRACTIONf_angle_d1.0985497
X-RAY DIFFRACTIONf_dihedral_angle_d3.3942272
X-RAY DIFFRACTIONf_chiral_restr0.096695
X-RAY DIFFRACTIONf_plane_restr0.008734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.01140.2973400.28466340X-RAY DIFFRACTION100
1.0114-1.02330.29743270.25886365X-RAY DIFFRACTION100
1.0233-1.03570.22943670.23166251X-RAY DIFFRACTION100
1.0357-1.04890.23513370.21756360X-RAY DIFFRACTION100
1.0489-1.06270.22723310.20616316X-RAY DIFFRACTION100
1.0627-1.07720.2313400.19566309X-RAY DIFFRACTION100
1.0772-1.09260.20743240.17996333X-RAY DIFFRACTION100
1.0926-1.10890.20963200.16256307X-RAY DIFFRACTION100
1.1089-1.12620.17243180.1556408X-RAY DIFFRACTION100
1.1262-1.14470.1813410.14626308X-RAY DIFFRACTION100
1.1447-1.16450.17263380.14576310X-RAY DIFFRACTION100
1.1645-1.18560.18173240.14716348X-RAY DIFFRACTION100
1.1856-1.20840.15683420.14226367X-RAY DIFFRACTION100
1.2084-1.23310.17373510.1386315X-RAY DIFFRACTION100
1.2331-1.25990.17512970.13686326X-RAY DIFFRACTION100
1.2599-1.28920.16723280.13886310X-RAY DIFFRACTION100
1.2892-1.32150.16823030.13556412X-RAY DIFFRACTION100
1.3215-1.35720.15663170.13056374X-RAY DIFFRACTION100
1.3572-1.39710.1713300.13186312X-RAY DIFFRACTION100
1.3971-1.44220.15813460.12916339X-RAY DIFFRACTION100
1.4422-1.49380.17873060.12696353X-RAY DIFFRACTION100
1.4938-1.55360.16823410.12986328X-RAY DIFFRACTION100
1.5536-1.62430.17373290.136414X-RAY DIFFRACTION100
1.6243-1.70990.17173260.14026324X-RAY DIFFRACTION100
1.7099-1.81710.173510.15216351X-RAY DIFFRACTION100
1.8171-1.95740.15173300.14336379X-RAY DIFFRACTION100
1.9574-2.15430.15193060.13936388X-RAY DIFFRACTION100
2.1543-2.4660.17113260.15826386X-RAY DIFFRACTION100
2.466-3.10680.17623260.16656403X-RAY DIFFRACTION100
3.1068-39.70670.15393290.14566477X-RAY DIFFRACTION99

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