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- PDB-5di5: beta1 t801 loop variant in P3221 -

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Basic information

Entry
Database: PDB / ID: 5di5
Titlebeta1 t801 loop variant in P3221
Componentsbeta1 t801 loop variant
KeywordsDE NOVO PROTEIN / synthetic protein / protein design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsMacDonald, J.T. / Kabasakal, B.V. / Murray, 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
DepositionAug 31, 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 1, 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 t801 loop variant


Theoretical massNumber of molelcules
Total (without water)25,4801
Polymers25,4801
Non-polymers00
Water34219
1
A: beta1 t801 loop variant

A: beta1 t801 loop variant


Theoretical massNumber of molelcules
Total (without water)50,9602
Polymers50,9602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area1370 Å2
ΔGint-15 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.460, 123.460, 47.830
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 t801 loop variant


Mass: 25479.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pRSETA-thr / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.13 Å3/Da / Density % sol: 70.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10mg /ml protein solution mixed with equal volume of 0.2 M ammonium acetate, 0.1 M Bis Tris pH 5.5, 45% v/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.28→106.92 Å / Num. all: 19284 / Num. obs: 19284 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 15.3
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.449 / Mean I/σ(I) obs: 1.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: theoretical protein model

Resolution: 2.28→53.46 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 919 4.77 %random
Rwork0.178 ---
obs0.1784 19259 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→53.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 0 19 1389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071380
X-RAY DIFFRACTIONf_angle_d1.4081878
X-RAY DIFFRACTIONf_dihedral_angle_d15.876480
X-RAY DIFFRACTIONf_chiral_restr0.059223
X-RAY DIFFRACTIONf_plane_restr0.009261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2801-2.40030.32451470.26582557X-RAY DIFFRACTION99
2.4003-2.55060.26051360.24672562X-RAY DIFFRACTION99
2.5506-2.74760.2391060.22552609X-RAY DIFFRACTION99
2.7476-3.02410.20891230.19532626X-RAY DIFFRACTION100
3.0241-3.46160.2341360.18792610X-RAY DIFFRACTION100
3.4616-4.36090.14231320.14362653X-RAY DIFFRACTION100
4.3609-53.47440.16141390.16522723X-RAY DIFFRACTION100
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)
18.0675-1.53943.18514.40810.27591.86540.44210.83531.0558-1.32450.2719-0.0205-0.0836-0.3213-0.72180.8266-0.06880.00680.66340.13150.587562.6265-18.9633-26.9891
24.48790.99211.27824.5763-1.65839.4241-0.18370.29150.0156-0.01660.2333-0.1472-0.6210.1652-0.05870.3612-0.06690.04380.37370.02020.404661.8205-19.8733-17.5711
35.7807-2.52024.76463.5673-3.48134.6921-0.00790.4853-0.0287-0.1499-0.04530.01910.0410.73320.03050.4577-0.00090.04220.46420.0310.446263.3961-27.7322-19.5309
43.9099-0.3351-0.06895.21350.98166.80050.09560.05610.1324-0.31760.02560.0344-0.4828-0.0655-0.07950.41520.00310.01350.38230.00940.40256.6904-24.094-15.7784
52.51311.05380.17373.30140.9045.7951-0.074-0.02980.36030.1031-0.01520.1996-0.3344-0.0310.10130.37860.05380.01290.41140.01540.463452.3134-26.7038-13.748
66.7365-0.88931.99743.2981-0.92057.1524-0.0814-0.19760.33540.034-0.01540.3307-0.5356-0.32130.01540.38690.03620.02510.42480.01520.447246.1569-27.5718-14.1795
72.36610.1733-0.89233.35751.91214.1665-0.03880.1603-0.0510.0264-0.03260.2137-0.0201-0.35790.08420.41180.01380.01470.51010.04460.487242.6513-34.849-12.1605
83.1879-5.51091.82259.842-1.65196.13160.3106-0.5203-0.26190.33150.16360.4553-0.1314-0.4067-0.30710.4078-0.10220.03860.54530.04460.46839.7717-35.376-7.3857
92.3531-0.1931-0.14483.09210.1913.02310.3638-0.4103-0.1136-0.0751-0.22580.23280.0378-0.7029-0.10220.3513-0.08850.0440.60260.04080.457835.4168-40.5345-10.5676
106.8934-0.7609-2.08444.8801-0.47014.97390.24980.32940.17020.0025-0.0969-0.2136-0.0868-0.19990.01240.4574-0.1428-0.03870.64990.040.523231.229-48.3706-6.3234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 49:55)
2X-RAY DIFFRACTION2(chain A and resseq 56:73)
3X-RAY DIFFRACTION3(chain A and resseq 74:81)
4X-RAY DIFFRACTION4(chain A and resseq 82:103)
5X-RAY DIFFRACTION5(chain A and resseq 104:128)
6X-RAY DIFFRACTION6(chain A and resseq 129:164)
7X-RAY DIFFRACTION7(chain A and resseq 165:186)
8X-RAY DIFFRACTION8(chain A and resseq 187:199)
9X-RAY DIFFRACTION9(chain A and resseq 200:223)
10X-RAY DIFFRACTION10(chain A and resseq 224:241)

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