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- PDB-5cwn: Crystal structure of de novo designed helical repeat protein DHR71 -

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Basic information

Entry
Database: PDB / ID: 5cwn
TitleCrystal structure of de novo designed helical repeat protein DHR71
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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

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Assembly

Deposited unit
A: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4055
Polymers23,6151
Non-polymers7904
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.270, 82.910, 103.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Designed helical repeat protein


Mass: 23614.760 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES, pH 9.5, 50% (v/v) PEG 200

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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: Jan 16, 2015
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: 1.7→50 Å / Num. obs: 22958 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 26.68 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.086 / Χ2: 0.985 / Net I/σ(I): 15.01 / Num. measured all: 158634
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
1.7-1.747.10.6381.6431.2511791166716661.77599.9
1.74-1.790.7631.3351.6111662165916561.44399.8
1.79-1.840.7221.1181.9810833153915351.20999.7
1.84-1.90.8530.8742.6610886153615340.94599.9
1.9-1.960.920.6183.9410551149814980.668100
1.96-2.030.9420.4575.410203143414340.494100
2.03-2.110.9510.3546.9510062143014280.38499.9
2.11-2.190.9850.22210.379245131413090.24199.6
2.19-2.290.990.16813.169193130213020.182100
2.29-2.40.9940.12916.248665124212360.13999.5
2.4-2.530.9930.11817.488407120011980.12899.8
2.53-2.690.9970.08720.997722112111150.09599.5
2.69-2.870.9980.07225.317421107910710.07899.3
2.87-3.10.9980.06128.4766289779750.06699.8
3.1-3.40.9980.05432.7762059379310.05999.4
3.4-3.80.9990.03939.6853848468410.04299.4
3.8-4.390.9990.03244.8748587477430.03599.5
4.39-5.380.9990.0344.5841856516500.03399.8
5.38-7.60.9990.03239.7232095305280.03699.6
7.60.9980.0338.6115243303080.03493.3

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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: 1.7→43.839 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1144 5 %RANDOM
Rwork0.1895 21747 --
obs0.1905 22891 99.62 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.74 Å2 / Biso mean: 45.6607 Å2 / Biso min: 17.08 Å2
Refinement stepCycle: final / Resolution: 1.7→43.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 123 49 1789
Biso mean--55.75 44.15 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081778
X-RAY DIFFRACTIONf_angle_d1.012373
X-RAY DIFFRACTIONf_chiral_restr0.039256
X-RAY DIFFRACTIONf_plane_restr0.004316
X-RAY DIFFRACTIONf_dihedral_angle_d13.39748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.77720.31111420.306826812823100
1.7772-1.87090.2761390.260126362775100
1.8709-1.98810.26151400.22226842824100
1.9881-2.14160.19941430.180826972840100
2.1416-2.35710.15981420.147227042846100
2.3571-2.69810.17961410.151726942835100
2.6981-3.39910.22981470.191627612908100
3.3991-43.85370.20281500.1942890304099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5231-0.2840.52661.69790.39231.6749-0.01480.1678-0.17590.0422-0.01530.06040.2444-0.0364-0.00010.1838-0.0162-0.00260.191-0.01560.21580.1145-14.191410.6887
21.78170.07050.07291.02881.28081.67010.0649-0.21990.09930.3259-0.08510.0326-0.0704-0.2003-0.00010.2838-0.0060.02430.259-0.04150.2385-3.8336-2.919427.8604
31.73550.1063-0.64430.76190.59591.1822-0.1237-0.65660.08980.39120.173-0.0868-0.1146-0.24980.16680.41570.04230.05460.4592-0.11080.263-7.3245-0.753742.9277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:99 )A1 - 99
2X-RAY DIFFRACTION2( CHAIN A AND RESID 100:175 )A100 - 175
3X-RAY DIFFRACTION3( CHAIN A AND RESID 176:207 )A176 - 207

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