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- PDB-5cwj: Crystal structure of de novo designed helical repeat protein DHR49 -

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Basic information

Entry
Database: PDB / ID: 5cwj
TitleCrystal structure of de novo designed helical repeat protein DHR49
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

Downloads & links

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Assembly

Deposited unit
A: Designed helical repeat protein


Theoretical massNumber of molelcules
Total (without water)19,5971
Polymers19,5971
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.890, 80.890, 46.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein Designed helical repeat protein


Mass: 19596.873 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-Potassium hydrogen phosphate, 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: 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: 16718 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 29.31 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.064 / Χ2: 0.978 / Net I/σ(I): 16 / Num. measured all: 121178
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
1.7-1.746.90.5361.3931.378632124612441.50799.8
1.74-1.790.761.1311.818664118211821.217100
1.79-1.840.8320.8232.448537115811570.88699.9
1.84-1.90.8950.6313.258394113611360.679100
1.9-1.960.9350.4344.638228111511150.467100
1.96-2.030.980.3076.287965107710770.33100
2.03-2.110.9920.1929.497630102610260.207100
2.11-2.190.9940.13612.9873219899890.146100
2.19-2.290.9960.10216.6268159249240.11100
2.29-2.40.9980.07520.4866058928920.081100
2.4-2.530.9980.07121.9664358798790.077100
2.53-2.690.9980.06224.9660728268260.067100
2.69-2.870.9990.05527.4754957587580.06100
2.87-3.10.9990.0530.6553597497490.054100
3.1-3.40.9990.04535.2145546526520.048100
3.4-3.80.9990.04237.4339925785780.046100
3.8-4.390.9990.03839.8137985595580.04299.8
4.39-5.380.9990.03839.9830654434420.04199.8
5.38-7.60.9990.03738.7324583583560.0499.4
7.60.9980.03839.8311592071780.04186

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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→40.45 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 788 5.02 %RANDOM
Rwork0.2003 14923 --
obs0.2021 15711 93.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.14 Å2 / Biso mean: 53.7052 Å2 / Biso min: 19.59 Å2
Refinement stepCycle: final / Resolution: 1.7→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 0 107 1377
Biso mean---49.81 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031456
X-RAY DIFFRACTIONf_angle_d0.5561963
X-RAY DIFFRACTIONf_chiral_restr0.027211
X-RAY DIFFRACTIONf_plane_restr0.002281
X-RAY DIFFRACTIONf_dihedral_angle_d13.774623
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.80650.42071180.31932155227381
1.8065-1.9460.32811250.26832356248190
1.946-2.14190.28591320.21632507263995
2.1419-2.45180.23071390.17832587272698
2.4518-3.08880.22231410.208426672808100
3.0888-40.46170.21891330.18542651278498
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)
11.24310.2286-0.10531.4913-0.52140.8440.6895-0.8511-0.45951.129-0.37350.86571.0882-0.43860.03050.6385-0.2259-0.05490.58830.14240.44596.694181.35234.6056
22.53770.44090.7051.4227-0.02453.51320.07510.0339-0.33320.22150.0222-0.10680.4313-0.16290.04340.3284-0.0526-0.04720.19170.03370.30510.660683.6517-8.5937
32.2727-0.7466-0.52071.56250.19231.6864-0.21930.91730.1014-0.24020.0958-0.2860.3079-0.0633-0.04140.3247-0.0972-0.02480.43640.04190.291711.910783.9417-23.8934
46.94370.49651.2724.6537-1.78432.0483-0.30442.83680.4354-1.5482-0.1186-0.05360.29550.3739-0.62020.3998-0.10790.08570.92320.04650.23716.358283.3034-32.4391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:20 )A2 - 20
2X-RAY DIFFRACTION2( CHAIN A AND RESID 21:99 )A21 - 99
3X-RAY DIFFRACTION3( CHAIN A AND RESID 100:142 )A100 - 142
4X-RAY DIFFRACTION4( CHAIN A AND RESID 143:161 )A143 - 161

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