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- PDB-5cwq: Crystal structure of de novo designed helical repeat protein DHR81 -

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Basic information

Entry
Database: PDB / ID: 5cwq
TitleCrystal structure of de novo designed helical repeat protein DHR81
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / 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)27,4687
Polymers26,9341
Non-polymers5346
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.000, 120.000, 120.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-302-

PO4

21A-302-

PO4

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Components

#1: Protein Designed helical repeat protein


Mass: 26933.738 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.08 M Sodium acetate, pH 4.6, 20% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2015
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 18193 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.9 % / Biso Wilson estimate: 31.42 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.312 / Rrim(I) all: 0.319 / Χ2: 0.936 / Net I/σ(I): 16.77 / Num. measured all: 397887
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
2.05-2.122.40.3213.5271.1429561131713173.608100
2.1-2.160.4572.6331.5929644132613262.694100
2.16-2.220.5832.211.9727707124312432.262100
2.22-2.290.6911.8932.5127407124312431.938100
2.29-2.370.7461.5493.2725957119611961.586100
2.37-2.450.8641.2934.2224267113511351.325100
2.45-2.540.9411.1026.3823589110611061.129100
2.54-2.650.9660.8318.9722463107310730.852100
2.65-2.760.9840.65412.4521953104110410.67100
2.76-2.90.9890.61314.05213349799790.628100
2.9-3.060.9950.50718.36213259519510.519100
3.06-3.240.9970.37921.98194448678670.387100
3.24-3.470.9980.25528.55189518508500.261100
3.47-3.740.9990.15836.51174197857850.162100
3.74-4.10.9990.10344.86155877097090.105100
4.1-4.580.9990.07950.48146816706700.081100
4.58-5.290.9990.09247.04128435865860.095100
5.29-6.480.9980.11442.85106784904900.116100
6.48-9.1710.04463.4385043943940.045100
9.1710.04165.545732352320.04298.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
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: 2.05→37.947 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 860 5 %RANDOM
Rwork0.1991 16326 --
obs0.2005 17186 94.47 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.51 Å2 / Biso mean: 51.3918 Å2 / Biso min: 20.58 Å2
Refinement stepCycle: final / Resolution: 2.05→37.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 44 63 1935
Biso mean--60.67 46.85 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021926
X-RAY DIFFRACTIONf_angle_d0.4252580
X-RAY DIFFRACTIONf_chiral_restr0.02275
X-RAY DIFFRACTIONf_plane_restr0.001359
X-RAY DIFFRACTIONf_dihedral_angle_d11.751770
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 (%)
2.05-2.17860.30281290.27952419254885
2.1786-2.34680.33451250.26852559268490
2.3468-2.58290.25931470.24252723287095
2.5829-2.95650.23151490.18792784293397
2.9565-3.72440.21541520.18092873302599
3.7244-37.95380.19461580.177829683126100
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)
12.57860.49050.20670.1980.11140.05170.3931-0.5641.52090.0794-0.03490.4116-0.68360.118-0.06430.7014-0.05680.08740.367-0.06850.5951-19.34540.484754.2818
20.1088-0.215-0.04241.32070.05311.28790.2164-0.3140.47510.0525-0.07560.0962-0.24060.1988-0.00080.4468-0.08130.04970.2768-0.00360.2788-18.029433.005651.0171
31.23130.1765-0.92491.2465-0.08291.11510.0525-0.52180.04920.2269-0.09870.0151-0.21580.312-0.02280.3824-0.10960.01010.360.03010.2289-15.983625.642155.3773
41.0952-0.46810.11631.645-0.94061.25160.2726-0.5037-0.95010.1163-0.2389-0.38090.5461-0.0576-0.14530.3898-0.0529-0.01260.30210.09630.3533-17.948813.913850.1665
50.41950.20350.14010.2761-0.33460.88050.21160.0185-0.5084-0.0331-0.1108-0.13490.07850.09640.00250.2946-0.0220.00320.29830.0330.2645-16.873918.727643.8392
65.5226-1.44970.84221.5666-0.44860.32160.40920.8392-1.1528-0.1092-0.18820.20730.41640.1759-0.0240.32210.0114-0.00230.2093-0.03450.2502-19.561514.254935.1345
70.3913-0.12610.59790.5805-0.43030.9910.13120.15640.4841-0.0641-0.1718-0.1799-0.084-0.032800.28390.0040.03670.26810.0340.2542-19.847223.084835.0397
80.83921.2365-0.1593.0825-2.38093.69860.24690.2043-0.5604-0.0254-0.6241-0.2289-0.41920.9251-0.3060.49760.16330.10690.874-0.12330.7316-0.911814.706533.1878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:30 )A4 - 30
2X-RAY DIFFRACTION2( CHAIN A AND RESID 31:57 )A31 - 57
3X-RAY DIFFRACTION3( CHAIN A AND RESID 58:116 )A58 - 116
4X-RAY DIFFRACTION4( CHAIN A AND RESID 117:144 )A117 - 144
5X-RAY DIFFRACTION5( CHAIN A AND RESID 145:173 )A145 - 173
6X-RAY DIFFRACTION6( CHAIN A AND RESID 174:201 )A174 - 201
7X-RAY DIFFRACTION7( CHAIN A AND RESID 202:226 )A202 - 226
8X-RAY DIFFRACTION8( CHAIN A AND RESID 227:236 )A227 - 236

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