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- PDB-5cwl: Crystal structure of de novo designed helical repeat protein DHR54 -

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Basic information

Entry
Database: PDB / ID: 5cwl
TitleCrystal structure of de novo designed helical repeat protein DHR54
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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
B: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9715
Polymers40,6032
Non-polymers3673
Water2,918162
1
A: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6694
Polymers20,3021
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Designed helical repeat protein


Theoretical massNumber of molelcules
Total (without water)20,3021
Polymers20,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.250, 69.100, 82.630
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: 20301.639 Da / Num. of mol.: 2
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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M Sodium chloride, 0.1 M Na/K phosphate, pH 6.2, 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: 1.5→50 Å / Num. obs: 51178 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 23.18 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 0.991 / Net I/σ(I): 15.08 / Num. measured all: 360741
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
1.5-1.547.10.4891.8021.0326354372337201.94699.9
1.54-1.580.4971.6591.1625799364236401.79299.9
1.58-1.630.581.3291.4825456358635841.43699.9
1.63-1.680.7521.0181.9524596345434521.09999.9
1.68-1.730.8090.8072.4523938335833560.87199.9
1.73-1.790.8790.5883.4123224324332410.63599.9
1.79-1.860.9580.4034.9322467313131290.43499.9
1.86-1.940.9710.2827.0221608301230100.30599.9
1.94-2.020.9860.18610.3620931291029080.299.9
2.02-2.120.9940.11415.6120154281428110.12399.9
2.12-2.240.9970.08420.3518855263326310.09199.9
2.24-2.370.9980.06525.5917994252325210.0799.9
2.37-2.540.9980.05429.2116770236923670.05999.9
2.54-2.740.9980.04933.1415399220321950.05299.6
2.74-30.9990.04237.1314056205620440.04599.4
3-3.350.9990.03839.8512548187218640.04199.6
3.35-3.870.9990.03444.8111171165016430.03699.6
3.87-4.740.9990.03246.769336142114080.03599.1
4.74-6.710.9990.03245.037307113211220.03599.1
6.710.9980.03140.5327786755320.03578.8

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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: 1.5→45.929 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 1817 3.88 %RANDOM
Rwork0.1793 45067 --
obs0.1805 46884 91.32 %-
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.29 Å2 / Biso mean: 47.768 Å2 / Biso min: 18.79 Å2
Refinement stepCycle: final / Resolution: 1.5→45.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 55 162 2920
Biso mean--72.65 49.43 -
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043019
X-RAY DIFFRACTIONf_angle_d0.6984086
X-RAY DIFFRACTIONf_chiral_restr0.028468
X-RAY DIFFRACTIONf_plane_restr0.002566
X-RAY DIFFRACTIONf_dihedral_angle_d12.6011224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.54060.45691130.35882828294176
1.5406-1.58590.36981140.3332944305878
1.5859-1.63710.30961230.29613095321882
1.6371-1.69560.31041210.26863185330685
1.6956-1.76350.31531370.24813297343488
1.7635-1.84380.22931430.21673430357391
1.8438-1.9410.19791370.20143533367094
1.941-2.06260.21881540.17753703385798
2.0626-2.22190.18311530.15653756390999
2.2219-2.44550.16521530.14937753928100
2.4455-2.79930.19351540.15733799395399
2.7993-3.52660.18471580.171238504008100
3.5266-45.95040.21441570.17143872402996
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)
10.2913-0.0099-0.05120.20390.08240.09090.08670.07250.0539-0.25910.56860.75420.045-0.9378-0.00050.3537-0.028-0.05050.60890.08140.5007-16.600212.7061-21.7028
20.5856-0.10220.64562.0188-0.35151.10620.05590.0704-0.0464-0.2064-0.0854-0.10890.0439-0.055800.22350.02610.01070.23330.00580.2263-7.336918.4977-15.159
30.6194-0.58210.54151.81920.57831.51760.06530.01060.01390.0432-0.1106-0.2986-0.03570.10400.1945-0.0056-0.00030.23110.02260.2248-1.356427.6251-4.6919
40.6085-0.8802-0.27321.573-0.09721.01820.15060.27960.25590.105-0.3253-1.1471-0.13650.9617-0.03150.344-0.0658-0.05860.50530.08190.49336.653330.7538-1.7293
50.0777-0.1506-0.0030.47430.41242.2173-0.12530.5040.2461-0.46390.03120.41820.1436-0.8787-0.45960.3970.0104-0.14360.57990.13720.3214-36.055726.642-22.127
61.30070.21790.38540.65-0.83481.73460.07940.5636-0.1467-1.220.0848-0.51320.3781-0.18760.770.62520.08710.18620.45280.03890.3489-25.975125.3873-21.278
70.3398-0.321-0.11050.89210.5650.36630.11070.3650.2378-0.31770.38730.3229-0.4184-0.8640.00930.32410.0590.03350.3530.09920.2446-32.559332.9566-14.9317
80.6825-0.348-0.00921.64810.65331.82910.04880.11060.1681-0.27990.0077-0.4267-0.2810.27420.00030.26030.01110.06040.26590.04360.3061-23.027633.8618-7.885
90.668-0.22120.31360.46760.33480.56930.15630.12990.17520.13090.00810.0558-0.7253-0.1890.00010.40150.01920.04590.2330.02030.3078-25.656843.13550.6632
100.39430.4333-0.00490.85670.31190.2752-0.2043-0.21780.10180.1801-0.0411-0.6672-0.12180.4974-0.01190.2769-0.0574-0.00880.35820.02830.4536-15.503939.42193.826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:22 )A2 - 22
2X-RAY DIFFRACTION2( CHAIN A AND RESID 23:109 )A23 - 109
3X-RAY DIFFRACTION3( CHAIN A AND RESID 110:154 )A110 - 154
4X-RAY DIFFRACTION4( CHAIN A AND RESID 155:178 )A155 - 178
5X-RAY DIFFRACTION5( CHAIN B AND RESID 2:23 )B2 - 23
6X-RAY DIFFRACTION6( CHAIN B AND RESID 24:45 )B24 - 45
7X-RAY DIFFRACTION7( CHAIN B AND RESID 46:66 )B46 - 66
8X-RAY DIFFRACTION8( CHAIN B AND RESID 67:131 )B67 - 131
9X-RAY DIFFRACTION9( CHAIN B AND RESID 132:154 )B132 - 154
10X-RAY DIFFRACTION10( CHAIN B AND RESID 155:176 )B155 - 176

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