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- PDB-4ycq: Beta1 synthetic solenoid protein -

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Basic information

Entry
Database: PDB / ID: 4ycq
TitleBeta1 synthetic solenoid protein
Componentsbeta1 protein
KeywordsSTRUCTURAL PROTEIN / solenoid / scaffold
Function / homologyE3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.405 Å
AuthorsMurray, J.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
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: beta1 protein


Theoretical massNumber of molelcules
Total (without water)24,6761
Polymers24,6761
Non-polymers00
Water54030
1
A: beta1 protein

A: beta1 protein


Theoretical massNumber of molelcules
Total (without water)49,3522
Polymers49,3522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area1500 Å2
ΔGint-12 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.420, 125.420, 47.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein beta1 protein


Mass: 24676.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): KRX
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.41 Å3/Da / Density % sol: 72.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: 0.1 M CAPS pH 10.5, 40% (v/v) MPD / PH range: 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0403 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0403 Å / Relative weight: 1
ReflectionResolution: 2.4→47.92 Å / Num. all: 16977 / Num. obs: 16977 / % possible obs: 99.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.66 % / Rmerge(I) obs: 0.087 / Net I/av σ(I): 15.3487 / Net I/σ(I): 5.7859
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 11.39 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 3.01 / % possible all: 99.02

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YC5

4yc5


Resolution: 2.405→41.053 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 858 5.06 %
Rwork0.1708 --
obs0.1726 16941 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.405→41.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 0 30 1355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071344
X-RAY DIFFRACTIONf_angle_d0.9631831
X-RAY DIFFRACTIONf_dihedral_angle_d17.173470
X-RAY DIFFRACTIONf_chiral_restr0.038218
X-RAY DIFFRACTIONf_plane_restr0.004255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4051-2.55570.24551410.20072648X-RAY DIFFRACTION99
2.5557-2.7530.28681360.21092645X-RAY DIFFRACTION99
2.753-3.030.24381580.18552661X-RAY DIFFRACTION100
3.03-3.46830.22941420.1892690X-RAY DIFFRACTION100
3.4683-4.36890.17671320.14162697X-RAY DIFFRACTION99
4.3689-41.05930.18851490.16952742X-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)
10.07190.1047-0.02360.1336-0.05370.075-0.03950.5272-0.1984-0.17780.00180.1754-0.19890.1552-0.00020.5954-0.07020.02210.59670.05440.5363.0411-20.111-17.9175
20.18270.1726-0.01910.1455-0.03680.0589-0.08380.08990.27020.14360.0521-0.1553-0.37540.1466-0.00020.4550.0010.00730.44370.03490.455559.583-23.5653-17.5937
30.31710.2490.08490.2555-0.0850.44150.01490.01920.01350.00610.06930.0717-0.1717-0.0039-00.43870.06-0.02930.44210.02040.434351.1929-30.0293-14.9743
40.04710.0544-0.01630.0551-0.020.01790.2339-0.19490.24490.297-0.20220.15560.0306-0.1457-0.00010.47860.0637-0.00710.60160.01980.568441.7461-31.2884-7.8535
50.0428-0.0112-0.02970.05540.03370.02850.10920.26-0.01760.0344-0.1246-0.0350.1364-0.4213-0.00060.4073-0.0028-0.02010.66030.00060.523443.6108-40.8249-15.3448
60.04440.01440.00090.02640.02340.0340.12650.23490.09210.1734-0.15040.2816-0.0287-0.2805-0.00050.42930.0340.05990.69370.03670.489737.8651-33.8449-6.7941
70.02580.0276-0.00530.04390.02410.0386-0.2810.1309-0.0499-0.2725-0.123-0.05730.1115-0.3181-0.0010.5055-0.0833-0.0010.56040.03970.620439.5209-43.4308-14.545
80.0812-0.209-0.03230.67980.0490.05690.3767-0.276-0.4025-0.1764-0.2721-0.1340.1332-0.4320.00730.3328-0.14660.04820.68910.04680.51334.5398-42.187-9.1305
90.0204-0.0102-0.01740.0330.04430.05040.3103-0.40920.12940.2515-0.0819-0.0139-0.2852-0.208-0.00030.5088-0.154-0.00960.65860.06790.499430.4189-49.8612-3.8541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 171 )
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 181 )
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 191 )
7X-RAY DIFFRACTION7chain 'A' and (resid 192 through 201 )
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 218 )
9X-RAY DIFFRACTION9chain 'A' and (resid 219 through 234 )

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