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- PDB-5cwh: Crystal structure of de novo designed helical repeat protein DHR14 -

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Basic information

Entry
Database: PDB / ID: 5cwh
TitleCrystal structure of de novo designed helical repeat protein DHR14
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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)19,7063
Polymers19,5821
Non-polymers1242
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.960, 104.390, 90.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Designed helical repeat protein


Mass: 19582.172 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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Lithium nitrate, 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: 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: 1.3→50 Å / Num. obs: 47853 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 20.2 % / Biso Wilson estimate: 16.06 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.082 / Χ2: 1.018 / Net I/σ(I): 19.19 / Num. measured all: 964864
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
1.3-1.33170.8472.5051.4959409350134952.58299.8
1.33-1.370.9131.958266803344434402.01199.9
1.37-1.410.9181.742.2765659332833231.78599.8
1.41-1.450.9631.213.263820321832161.24299.9
1.45-1.50.9890.6645.2462282312431180.68199.8
1.5-1.550.9920.5016.7961092304230390.51499.9
1.55-1.610.9970.4058.1759114292929260.41599.9
1.61-1.680.9970.3289.9157482282028180.33699.9
1.68-1.750.9980.2711.8256128272927280.277100
1.75-1.840.9990.19614.9753413257725770.2100
1.84-1.940.9990.1517.9152057248824850.15499.9
1.94-2.060.9990.125.1450085236723670.103100
2.06-2.210.07134.3546590218521840.073100
2.2-2.3710.06241.3844291208620840.06399.9
2.37-2.610.05845.5940396191219120.06100
2.6-2.9110.04951.235675172817230.05199.7
2.91-3.360.9990.04658.4232797155015470.04799.8
3.36-4.110.9990.04269.4927245131713040.04399
4.11-5.810.9990.0426920272104210180.04397.7
5.8110.04267.27102546205490.04388.5

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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: 1.3→38.13 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 2377 5 %RANDOM
Rwork0.1606 45173 --
obs0.1619 47550 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.08 Å2 / Biso mean: 31.1042 Å2 / Biso min: 8.99 Å2
Refinement stepCycle: final / Resolution: 1.3→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1255 0 20 209 1484
Biso mean--28.04 43.44 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091454
X-RAY DIFFRACTIONf_angle_d1.0961977
X-RAY DIFFRACTIONf_chiral_restr0.067239
X-RAY DIFFRACTIONf_plane_restr0.004263
X-RAY DIFFRACTIONf_dihedral_angle_d12.409593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.32670.37411400.31092632277299
1.3267-1.35560.3021370.27922625276299
1.3556-1.38710.31751370.24552623276099
1.3871-1.42180.29771400.223926512791100
1.4218-1.46030.21591390.19122624276399
1.4603-1.50320.18611370.16592608274598
1.5032-1.55170.17371380.13582649278799
1.5517-1.60720.17381390.12952639277899
1.6072-1.67160.18681360.12642624276099
1.6716-1.74760.15091420.12032672281499
1.7476-1.83980.15671390.12392637277699
1.8398-1.9550.17841420.12682664280699
1.955-2.1060.15581390.11842661280099
2.106-2.31790.14381430.121526902833100
2.3179-2.65320.15221430.136327092852100
2.6532-3.34250.19311420.16422716285899
3.3425-38.14620.20251440.19992749289396

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