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- PDB-4yc5: Beta1 synthetic solenoid protein -

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Basic information

Entry
Database: PDB / ID: 4yc5
TitleBeta1 synthetic solenoid protein
Componentsbeta1
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 / MIR / Resolution: 1.755 Å
AuthorsMurray, J.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/F023308/1 United Kingdom
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 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7473
Polymers24,6761
Non-polymers712
Water4,918273
1
A: beta1
hetero molecules

A: beta1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4946
Polymers49,3522
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,-y-1,-z+1/21
Buried area1950 Å2
ΔGint-46 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.570, 64.570, 160.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21A-625-

HOH

31A-627-

HOH

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Components

#1: Protein beta1


Mass: 24676.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: synthetic protein sequence / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): KRX
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.39 Å3/Da / Density % sol: 63.69 % / Description: long rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis Tris, 3.0 M sodium chloride. / PH range: 5.5

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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: 1.75→64.57 Å / Num. all: 34852 / Num. obs: 34852 / % possible obs: 99.71 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/av σ(I): 22.3587 / Net I/σ(I): 7.2971
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 14.24 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.01 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MIR
Starting model: 3DU1

3du1


Resolution: 1.755→64.57 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 1750 5.03 %
Rwork0.1576 --
obs0.159 34786 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.755→64.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 2 273 1860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061616
X-RAY DIFFRACTIONf_angle_d0.9812199
X-RAY DIFFRACTIONf_dihedral_angle_d14.175571
X-RAY DIFFRACTIONf_chiral_restr0.042257
X-RAY DIFFRACTIONf_plane_restr0.004305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7549-1.80650.2381480.19362681X-RAY DIFFRACTION100
1.8065-1.86480.22881340.18472710X-RAY DIFFRACTION100
1.8648-1.93150.23881400.17372703X-RAY DIFFRACTION100
1.9315-2.00880.15741450.15082712X-RAY DIFFRACTION100
2.0088-2.10030.17991580.14152695X-RAY DIFFRACTION100
2.1003-2.2110.17321460.14182711X-RAY DIFFRACTION100
2.211-2.34950.1621400.14052728X-RAY DIFFRACTION99
2.3495-2.53090.16381300.15282759X-RAY DIFFRACTION100
2.5309-2.78560.1951420.17052764X-RAY DIFFRACTION100
2.7856-3.18870.20431520.16712785X-RAY DIFFRACTION100
3.1887-4.01740.17641770.14232807X-RAY DIFFRACTION100
4.0174-64.61370.17581380.16612981X-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)
12.4438-1.1631-0.4874.14740.04622.18520.0450.5217-0.214-0.3463-0.10710.12940.2208-0.46210.07130.1337-0.01010.00580.2791-0.00850.138418.7644-17.2504-14.7474
23.32653.4391-0.03257.8838-0.21830.6096-0.10720.35440.1224-0.54170.07830.29770.1184-0.29210.00570.1315-0.0215-0.02280.27460.01930.12249.5249-18.6277-11.4096
37.5269-4.08423.25932.9797-2.39014.6278-0.0850.0511-0.4759-0.2618-0.08950.17990.4141-0.14240.14880.26090.04380.0480.3164-0.03850.185716.9152-29.9676-10.5289
41.2641.31820.15591.6665-0.37530.95490.00720.20010.0185-0.2181-0.0618-0.10350.23210.09060.03380.12070.03580.01450.21580.01140.123815.5713-22.627-5.7314
54.07662.50680.46912.94862.80854.87370.0096-0.075-0.18780.1827-0.0352-0.57550.19650.3250.02460.16040.0779-0.00040.28120.05040.14722.9714-26.4101-1.6631
60.54520.1979-0.0050.8575-0.37421.87410.00620.0407-0.0128-0.02270.01990.0180.145-0.0742-0.02580.09150.0058-0.00930.12490.00690.121712.3356-26.36548.6614
72.0206-0.7839-0.64992.62883.4834.70150.0463-0.02090.06820.15120.0696-0.37210.03510.2305-0.10180.13960.0015-0.00410.12020.01410.140217.6197-29.588521.7322
82.17710.01180.5144.36970.26312.29740.05280.0423-0.005-0.1099-0.03640.15170.0372-0.1953-0.02210.1039-0.01010.00010.13990.04010.10047.2215-29.891822.1306
90.53160.01110.02880.9462-0.11530.76250.0266-0.06680.02620.10490.03470.02530.0406-0.087-0.0520.1288-0.0029-0.0040.10810.01350.11979.9437-30.256529.1073
101.78790.06020.13963.1234-1.50372.6748-0.03360.0547-0.0087-0.23810.27880.24780.2173-0.4924-0.21980.1247-0.0329-0.00590.1650.040.12633.452-34.446537.6651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 21:33)
2X-RAY DIFFRACTION2(chain A and resseq 34:40)
3X-RAY DIFFRACTION3(chain A and resseq 41:45)
4X-RAY DIFFRACTION4(chain A and resseq 46:63)
5X-RAY DIFFRACTION5(chain A and resseq 64:70)
6X-RAY DIFFRACTION6(chain A and resseq 71:165)
7X-RAY DIFFRACTION7(chain A and resseq 166:172)
8X-RAY DIFFRACTION8(chain A and resseq 173:186)
9X-RAY DIFFRACTION9(chain A and resseq 187:215)
10X-RAY DIFFRACTION10(chain A and resseq 216:233)

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