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- PDB-5cwi: Crystal structure of de novo designed helical repeat protein DHR18 -

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Basic information

Entry
Database: PDB / ID: 5cwi
TitleCrystal structure of de novo designed helical repeat protein DHR18
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: 1.75 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)27,1392
Polymers27,0441
Non-polymers951
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.920, 43.650, 48.750
Angle α, β, γ (deg.)116.560, 90.720, 102.190
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Designed helical repeat protein


Mass: 27044.129 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M Phosphate-citrate, pH 4.2, 40% (v/v) PEG 300

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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: 1.75→50 Å / Num. obs: 17261 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 26.83 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.063 / Χ2: 0.943 / Net I/σ(I): 9.82 / Num. measured all: 36231
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
1.75-1.82.10.5390.8491.132656132212471.16794.3
1.8-1.840.6250.6251.492520128312020.86593.7
1.84-1.90.6430.5861.552572129412200.80994.3
1.9-1.960.7910.4132.282473122111610.56895.1
1.96-2.020.8810.283.12353117411160.38795.1
2.02-2.090.9310.2044.162379117511220.28195.5
2.09-2.170.9490.1585.322202109910530.21995.8
2.17-2.260.9790.1047.442224108210410.14396.2
2.26-2.360.9850.0869.2119909939530.11996
2.36-2.470.990.06510.9202810029650.0996.3
2.47-2.610.990.06211.5918429158840.08596.6
2.61-2.770.9940.05313.3918379008710.07296.8
2.77-2.960.9970.03616.7916148147880.04996.8
2.96-3.20.9950.03718.4215677787620.05197.9
3.2-3.50.9960.03221.1514107166970.04397.3
3.5-3.910.9970.02425.3512926366230.03398
3.91-4.520.9980.02226.9211975725650.0398.8
4.52-5.530.9990.01925.39834774690.02598.3
5.53-7.830.9990.02127.067613733590.02896.2
7.830.9990.0227.733311991630.02781.9

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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: 1.75→43.277 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 866 5.02 %RANDOM
Rwork0.2024 16380 --
obs0.2035 17246 95.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.79 Å2 / Biso mean: 38.4103 Å2 / Biso min: 18.01 Å2
Refinement stepCycle: final / Resolution: 1.75→43.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 5 64 1805
Biso mean--50.68 45.14 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031990
X-RAY DIFFRACTIONf_angle_d0.4972692
X-RAY DIFFRACTIONf_chiral_restr0.024291
X-RAY DIFFRACTIONf_plane_restr0.002377
X-RAY DIFFRACTIONf_dihedral_angle_d12.669802
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 (%)
1.75-1.85990.39721330.34112649278294
1.8599-2.00350.31481490.27392707285695
2.0035-2.20510.26751450.22322729287496
2.2051-2.52410.21971420.18862762290497
2.5241-3.180.21951480.19832761290997
3.18-43.29010.18891490.18022772292197
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)
10.90390.0576-0.00310.15620.31330.6434-0.1234-0.11880.40050.1293-0.26370.3168-0.4054-0.4859-0.13140.3210.014-0.02520.3034-0.05330.37111.08053.669118.2975
20.7155-0.2615-0.2871.38180.69170.38640.00470.12180.0641-0.15290.2244-0.2401-0.30710.70.00910.2705-0.05760.00010.3191-0.00850.27119.61240.119315.7951
30.82530.0713-0.08851.7684-1.1351.2036-0.0333-0.08830.0426-0.14990.01860.20330.2415-1.1052-0.00350.2044-0.01360.00430.2631-0.00690.26199.4934-5.4213.9066
40.6638-0.2721-1.12222.9157-0.21762.3046-0.00380.03870.1033-0.16010.1031-0.06290.04740.1796-0.00120.1665-0.0009-0.00290.1862-0.00270.207115.623-11.231814.6318
50.99160.35850.17641.8208-0.36581.4084-0.0705-0.0218-0.0836-0.08520.1171-0.07150.11890.10930.00020.2640.0049-0.01850.22270.00560.248716.1098-20.513714.189
60.7130.28890.4850.9632-0.59111.0631-0.44920.3175-0.69270.09780.1087-0.35160.99190.1792-0.00140.6228-0.03670.05940.4132-0.07430.477916.2395-27.860918.3725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:27 )A2 - 27
2X-RAY DIFFRACTION2( CHAIN A AND RESID 28:57 )A28 - 57
3X-RAY DIFFRACTION3( CHAIN A AND RESID 58:87 )A58 - 87
4X-RAY DIFFRACTION4( CHAIN A AND RESID 88:147 )A88 - 147
5X-RAY DIFFRACTION5( CHAIN A AND RESID 148:207 )A148 - 207
6X-RAY DIFFRACTION6( CHAIN A AND RESID 208:234 )A208 - 234

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