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- PDB-5cwg: Crystal structure of de novo designed helical repeat protein DHR10 -

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Basic information

Entry
Database: PDB / ID: 5cwg
TitleCrystal structure of de novo designed helical repeat protein DHR10
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Function / homologyUnknown ligand
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 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 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7133
Polymers23,6511
Non-polymers622
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.590, 50.560, 72.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

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Components

#1: Protein Designed helical repeat protein


Mass: 23651.416 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)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 1.84 Å3/Da / Density % sol: 33.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium formate, 20% (w/v) PEG 3350

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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: Dec 6, 2013
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: 1.2→50 Å / Num. obs: 54627 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 12.64 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.04 / Χ2: 0.979 / Net I/σ(I): 22.67 / Num. measured all: 313175
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
1.2-1.232.80.8060.5261.859802402335160.64487.4
1.23-1.260.8380.5062.3713443394938020.59596.3
1.26-1.30.930.4023.7118756384538410.45199.9
1.3-1.340.9570.364.9422987372137200.393100
1.34-1.390.9680.3025.9522430361536140.329100
1.39-1.430.980.2527.0121931351435130.275100
1.43-1.490.9930.15810.4721198338533830.17299.9
1.49-1.550.9950.11614.2420447325432540.127100
1.55-1.620.9960.116.4919853314431410.10999.9
1.62-1.70.9970.08519.6219100301230100.09399.9
1.7-1.790.9980.06823.9917940283428310.07499.9
1.79-1.90.9990.05229.7617268271227090.05799.9
1.9-2.030.9990.04137.416264257125680.04599.9
2.03-2.190.9990.03246.5415019238623840.03599.9
2.19-2.40.9990.02755.4713763221822150.0399.9
2.4-2.680.9990.02559.9812196200219990.02799.9
2.68-3.110.02164.8810800177717730.02399.8
3.1-3.7910.01971.529524153315250.02199.5
3.79-5.3710.01973.276975121911800.02196.8
5.370.9990.01965.5934797256490.02189.5

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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: 1.2→41.458 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1666 2730 5.01 %RANDOM
Rwork0.1344 51814 --
obs0.136 54544 98.47 %-
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.75 Å2 / Biso mean: 21.8278 Å2 / Biso min: 8.53 Å2
Refinement stepCycle: final / Resolution: 1.2→41.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 37 231 1787
Biso mean--27.66 33.46 -
Num. residues----195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091961
X-RAY DIFFRACTIONf_angle_d1.1082660
X-RAY DIFFRACTIONf_chiral_restr0.064279
X-RAY DIFFRACTIONf_plane_restr0.005380
X-RAY DIFFRACTIONf_dihedral_angle_d13.582820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.22060.3021060.28222214232085
1.2206-1.24280.28891270.24482420254794
1.2428-1.26670.2481380.2182505264397
1.2667-1.29260.23961360.17525902726100
1.2926-1.32070.19661260.15626012727100
1.3207-1.35140.20331490.143425832732100
1.3514-1.38520.18411290.143426062735100
1.3852-1.42260.17721440.130926092753100
1.4226-1.46450.18221380.117125912729100
1.4645-1.51180.1471310.100726192750100
1.5118-1.56580.12881450.09425972742100
1.5658-1.62850.141290.095126302759100
1.6285-1.70260.14951480.099426222770100
1.7026-1.79240.12021270.101526242751100
1.7924-1.90470.14841430.106326282771100
1.9047-2.05170.13581420.106226412783100
2.0517-2.25820.13481490.107226402789100
2.2582-2.58490.13761350.11626752810100
2.5849-3.25660.16551430.134826932836100
3.2566-41.4830.20311450.17772726287196

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