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- PDB-5cwm: Crystal structure of de novo designed helical repeat protein DHR64 -

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Basic information

Entry
Database: PDB / ID: 5cwm
TitleCrystal structure of de novo designed helical repeat protein DHR64
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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

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Assembly

Deposited unit
A: Designed helical repeat protein


Theoretical massNumber of molelcules
Total (without water)27,2341
Polymers27,2341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.280, 98.280, 48.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Designed helical repeat protein


Mass: 27233.951 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)

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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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Sodium acetate, pH 5.0, 10% (v/v) MPD

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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: 2.9→50 Å / Num. obs: 6086 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 72.93 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.159 / Χ2: 0.935 / Net I/σ(I): 14.38 / Num. measured all: 67571
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
2.9-2.9811.30.4392.1381.3450704484482.239100
2.98-3.060.5511.7491.7448214314311.832100
3.06-3.150.7511.4562.1447754234231.525100
3.15-3.240.7511.0742.8345424054051.125100
3.24-3.350.8490.8383.5644553943940.878100
3.35-3.470.9440.565.5743473873870.586100
3.47-3.60.9570.4127.1640943613610.431100
3.6-3.740.9730.3168.9341743753750.332100
3.74-3.910.980.26810.2838663443440.28100
3.91-4.10.9870.19114.2635593223220.201100
4.1-4.320.9940.12220.7435383163160.128100
4.32-4.590.9970.10424.0632902962960.109100
4.59-4.90.9960.123.9730862822820.105100
4.9-5.290.9960.1220.5229202662660.126100
5.29-5.80.9950.1220.4826162432430.126100
5.8-6.480.9970.10223.5922982152150.107100
6.48-7.490.9990.05536.7621361971970.058100
7.49-9.1710.03157.7918181681670.03399.4
9.17-12.9710.0368.2214061331330.032100
12.970.9990.03256.376082810.03498.8

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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: 2.9→49.14 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 277 4.91 %RANDOM
Rwork0.2159 5368 --
obs0.2175 5645 92.95 %-
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.81 Å2 / Biso mean: 99.6941 Å2 / Biso min: 41.82 Å2
Refinement stepCycle: final / Resolution: 2.9→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 0 0 1793
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021818
X-RAY DIFFRACTIONf_angle_d0.4192432
X-RAY DIFFRACTIONf_chiral_restr0.017280
X-RAY DIFFRACTIONf_plane_restr0.001329
X-RAY DIFFRACTIONf_dihedral_angle_d10.44758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.65370.36941280.29522510263888
3.6537-49.1470.21111490.18952858300798
Refinement TLS params.Method: refined / Origin x: 46.7183 Å / Origin y: -11.1232 Å / Origin z: -4.2469 Å
111213212223313233
T0.6972 Å2-0.0608 Å2-0.2034 Å2-0.5427 Å2-0.0635 Å2--0.4497 Å2
L3.7168 °2-1.3452 °2-0.8878 °2-6.4248 °20.4145 °2--4.2005 °2
S-0.1441 Å °0.2339 Å °0.1904 Å °0.0199 Å °-0.329 Å °0.3908 Å °-0.565 Å °-0.1339 Å °-0.0469 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 2:227 )

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