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- PDB-5dra: t3284 loop variant of beta1 -

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Basic information

Entry
Database: PDB / ID: 5dra
Titlet3284 loop variant of beta1
Components3beta1
KeywordsDE NOVO PROTEIN / synthetic protein / loop design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKabasakal, B.V. / MacDonald, J.T. / Murray, W.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.
Authors: MacDonald, J.T. / Kabasakal, B.V. / Godding, D. / Kraatz, S. / Henderson, L. / Barber, J. / Freemont, P.S. / Murray, J.W.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3beta1


Theoretical massNumber of molelcules
Total (without water)23,2011
Polymers23,2011
Non-polymers00
Water00
1
A: 3beta1

A: 3beta1


Theoretical massNumber of molelcules
Total (without water)46,4032
Polymers46,4032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1490 Å2
ΔGint-15 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.340, 48.340, 221.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 3beta1


Mass: 23201.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pRSETA / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 4.6 / Details: 1.1M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→48.45 Å / Num. obs: 5854 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 33.07
Reflection shellResolution: 3→3.08 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 14.06 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.227 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3071 251 4.34 %
Rwork0.2496 --
obs0.2522 5784 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→47.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 0 0 1416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111429
X-RAY DIFFRACTIONf_angle_d1.4461941
X-RAY DIFFRACTIONf_dihedral_angle_d17.59867
X-RAY DIFFRACTIONf_chiral_restr0.089228
X-RAY DIFFRACTIONf_plane_restr0.008267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9937-3.77160.35781270.26752675X-RAY DIFFRACTION99
3.7716-47.23320.28331240.24072858X-RAY DIFFRACTION98
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)
12.155-1.86391.39612.3702-4.023820.03690.728-0.4272-0.7865-0.2551-0.01510.23580.17160.22751.757-0.31020.36991.7087-0.54410.854412.7255-24.19532.9894
21.60230.6796-0.35320.8822-0.36030.1524-0.28420.64050.2357-0.01940.0888-0.4474-0.09380.252-0.04290.60510.0512-0.1192.235-0.25910.91438.4759-16.72016.2026
31.10250.57690.92991.16870.36863.052-0.00130.1079-0.21220.36940.1967-0.24711.25950.09450.01290.7964-0.05150.00271.6323-0.50840.65528.6015-23.48614.5815
40.89640.1154-0.33321.69391.19011.9133-0.1098-0.0797-0.03570.14810.3471-0.23710.12150.3476-0.01530.35760.0882-0.01231.424-0.2430.406513.0846-16.921418.0541
51.5281-1.12781.33714.3076-2.78045.74710.0284-0.37260.0085-0.15540.14380.04630.5826-0.2293-0.14010.5481-0.28770.08781.3368-0.28750.40342.3434-22.959921.5031
64.7906-0.6335-2.48083.5880.20612.4242-0.1885-0.0002-0.2136-0.11480.0748-0.37610.22610.287-0.04530.45640.08410.09231.317-0.38650.604212.358-16.285422.4938
70.50940.70811.2374.39870.15673.71760.3625-0.3687-0.0884-0.0464-0.07770.15990.7068-0.2376-0.34980.6782-0.1545-0.13731.1214-0.30640.47861.9851-21.475325.9964
87.20571.6406-1.14941.4017-1.23183.0854-0.30430.5445-1.0947-0.04880.1381-0.0620.36860.02380.17020.325-0.05410.07521.0668-0.40740.571510.6839-18.393529.7208
92.03760.7616-1.23790.285-0.47281.02510.0530.15690.53180.0823-0.05260.38960.1196-0.26750.04730.3246-0.23690.02870.9422-0.14650.51814.8148-11.737532.7623
102.94810.3296-0.17371.0921-0.1651.6121-0.02590.5567-0.2955-0.0607-0.08140.03760.1513-0.094-0.00560.0728-0.1197-0.03620.2878-0.01770.40938.4073-12.815544.4758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 24:28)
2X-RAY DIFFRACTION2(chain A and resid 29:41)
3X-RAY DIFFRACTION3(chain A and resid 42:66)
4X-RAY DIFFRACTION4(chain A and resid 67:78)
5X-RAY DIFFRACTION5(chain A and resid 79:85)
6X-RAY DIFFRACTION6(chain A and resid 86:98)
7X-RAY DIFFRACTION7(chain A and resid 99:105)
8X-RAY DIFFRACTION8(chain A and resid 106:133)
9X-RAY DIFFRACTION9(chain A and resid 134:143)
10X-RAY DIFFRACTION10(chain A and resid 144:213)

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