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- PDB-5cwk: Crystal structure of de novo designed helical repeat protein DHR53 -

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Basic information

Entry
Database: PDB / ID: 5cwk
TitleCrystal structure of de novo designed helical repeat protein DHR53
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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)20,5111
Polymers20,5111
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.380, 24.340, 60.440
Angle α, β, γ (deg.)90.000, 116.860, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Designed helical repeat protein


Mass: 20510.541 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 / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 2.2 / Details: 26% (w/v) PEG 6000, 0.1 M Sodium citrate, pH 2.2

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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: Nov 20, 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: 1.9→50 Å / Num. obs: 13327 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 38.04 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.057 / Χ2: 0.977 / Net I/σ(I): 13.15 / Num. measured all: 46741
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.953.60.7391.6680.9933819579491.96799.2
1.95-20.7781.1191.3935139859811.31899.6
2-2.060.9060.6772.2232849249190.79799.5
2.06-2.120.960.4623.0731799018930.54399.1
2.12-2.190.970.3693.8232098998980.43599.9
2.19-2.270.9840.255.4729908468340.29598.6
2.27-2.360.9860.1936.5529528278220.22799.4
2.36-2.450.9890.1677.4328678068000.19899.3
2.45-2.560.9920.1269.4526497537460.14999.1
2.56-2.690.9960.08812.4125917427330.10498.8
2.69-2.830.9960.07814.3723816936780.09297.8
2.83-30.9980.05717.5822936686630.06899.3
3-3.210.9980.04821.3621066206120.05798.7
3.21-3.470.9990.03626.2619685995900.04398.5
3.47-3.80.9990.0332.0717455375250.03697.8
3.8-4.250.9990.02439.4716874934790.02897.2
4.25-4.910.9990.02140.9514634434240.02595.7
4.91-6.010.9990.02238.1912463833730.02797.4
6.01-8.50.9990.0238.348532902680.02592.4
8.50.9990.02236.883841851400.02775.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→32.466 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 661 4.99 %RANDOM
Rwork0.2083 12573 --
obs0.2097 13234 97.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 249.45 Å2 / Biso mean: 73.2862 Å2 / Biso min: 32.92 Å2
Refinement stepCycle: final / Resolution: 1.9→32.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 0 22 1358
Biso mean---65.35 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031378
X-RAY DIFFRACTIONf_angle_d0.6441851
X-RAY DIFFRACTIONf_chiral_restr0.027208
X-RAY DIFFRACTIONf_plane_restr0.003251
X-RAY DIFFRACTIONf_dihedral_angle_d14.678584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-2.04610.44421300.3622469259998
2.0461-2.2520.30161290.26162486261598
2.252-2.57770.23351320.21112509264199
2.5777-3.24720.24381360.21762549268599
3.2472-32.47040.20811340.18392560269496
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)
11.8210.16881.33051.7668-0.55252.9172-0.13530.47750.1758-0.08850.0286-0.2029-0.35890.5989-0.00030.53880.0309-0.09940.51210.00590.449918.8092-2.316417.5641
22.3395-0.28940.36331.9333-0.40983.25790.2103-0.3138-0.06290.25540.05860.05410.3805-0.19270.00360.4698-0.0631-0.05570.40510.04910.3817-2.8353-3.729813.2388
30.4832-1.01-0.6153.14621.07570.87640.213-0.56270.1659-0.1648-0.55091.2717-0.2198-1.0749-0.06370.7089-0.11960.08740.9729-0.01270.7463-18.92422.05411.1707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:64 )A2 - 64
2X-RAY DIFFRACTION2( CHAIN A AND RESID 65:148 )A65 - 148
3X-RAY DIFFRACTION3( CHAIN A AND RESID 149:173 )A149 - 173

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