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- PDB-5cwd: Crystal structure of de novo designed helical repeat protein DHR7 -

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Basic information

Entry
Database: PDB / ID: 5cwd
TitleCrystal structure of de novo designed helical repeat protein DHR7
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å
AuthorsBhabha, G. / Ekiert, D.C.
CitationJournal: Nature / Year: 2015
Title: Exploring the repeat protein universe through computational protein design.
Authors: Brunette, T.J. / Parmeggiani, F. / Huang, P.S. / Bhabha, G. / Ekiert, D.C. / Tsutakawa, S.E. / Hura, G.L. / Tainer, J.A. / Baker, D.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 6, 2016Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list / reflns_shell
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed helical repeat protein


Theoretical massNumber of molelcules
Total (without water)19,1031
Polymers19,1031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.881, 29.449, 63.432
Angle α, β, γ (deg.)90.000, 123.510, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Designed helical repeat protein


Mass: 19102.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.2 M Sodium chloride, 0.1 M CHES, pH 9.5, 50% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.111 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2014
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.111 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 4124 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 55.6 Å2 / Rmerge F obs: 0.987 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.181 / Χ2: 0.947 / Net I/σ(I): 4.88 / Num. measured all: 13960
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.6-2.673.40.6250.8121.2110933293220.96497.9
2.67-2.740.7280.7441.349582742790.88100
2.74-2.820.760.5951.669792902860.7198.6
2.82-2.910.760.55429982972910.65898
2.91-30.8010.4712.48902582560.55699.2
3-3.110.8590.4392.468792562530.5298.8
3.11-3.230.9070.3153.538952662630.37498.9
3.23-3.360.9150.2794.58172432400.33198.8
3.36-3.510.9630.1985.457852272230.23398.2
3.51-3.680.9510.1696.648282452410.298.4
3.68-3.880.9450.1576.956531991960.18998.5
3.88-4.110.9690.1348.067302192140.15897.7
4.11-4.40.9860.137.596081821780.15397.8
4.4-4.750.9660.1187.965591791730.14296.6
4.75-5.20.9830.1078.595411671630.1397.6
5.2-5.810.9730.1198.514941581540.14397.5
5.81-6.710.980.1198.154081331280.14396.2
6.71-8.220.9880.0810.263751151140.09599.1
8.22-11.630.9910.07310.45315100970.08797
11.630.9920.0599.6615558530.07391.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→42.029 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.306 206 5 %RANDOM
Rwork0.259 3916 --
obs0.2613 4122 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.3 Å2 / Biso mean: 65.9897 Å2 / Biso min: 45.97 Å2
Refinement stepCycle: final / Resolution: 2.61→42.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 0 0 1251
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031275
X-RAY DIFFRACTIONf_angle_d0.5311700
X-RAY DIFFRACTIONf_chiral_restr0.022188
X-RAY DIFFRACTIONf_plane_restr0.002230
X-RAY DIFFRACTIONf_dihedral_angle_d13.074493
LS refinement shellResolution: 2.61→2.67 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.306 206 -
Rwork0.259 3916 -
all-4122 -
obs--99 %

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