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- PDB-5fin: DARPins as a new tool for experimental phasing in protein crystal... -

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Basic information

Entry
Database: PDB / ID: 5fin
TitleDARPins as a new tool for experimental phasing in protein crystallography
ComponentsNI3C DARPIN MUTANT5 HG-SITE N1
KeywordsMETAL BINDING PROTEIN / DARPIN / ENGINEERED PROTEIN / EXPERIMENTAL PHASING
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / :
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.34 Å
AuthorsBatyuk, A. / Honegger, A. / Andres, F. / Briand, C. / Gruetter, M. / Plueckthun, A.
CitationJournal: To be Published
Title: Darpins as a New Tool for Experimental Phasing in Protein Crystallography
Authors: Batyuk, A. / Honegger, A. / Andres, F. / Briand, C. / Gruetter, M. / Plueckthun, A.
History
DepositionSep 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NI3C DARPIN MUTANT5 HG-SITE N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7842
Polymers18,5841
Non-polymers2011
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.540, 50.870, 93.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NI3C DARPIN MUTANT5 HG-SITE N1


Mass: 18583.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DESIGNED ANKYRIN REPEAT PROTEIN WITH THREE INTERNAL REPEAT AND C-TERMINAL CAPPING REPEAT TYPE MUT5 AND ENGINEERED BURIED MERCURY BINDING SITE CYS30-CYS65 WITH BOUND HG-ION
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30SS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K12 / Variant (production host): XL1-BLUE
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.41 % / Description: NONE
Crystal growpH: 8 / Details: 25% W/V PEG 6000, 0.1M HEPES, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→46.5 Å / Num. obs: 7716 / % possible obs: 99.5 % / Observed criterion σ(I): 2.09 / Redundancy: 3.82 % / Biso Wilson estimate: 39.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.39
Reflection shellHighest resolution: 2.34 Å / Redundancy: 3.79 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.09 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.34→46.5 Å / SU ML: 0.31 / σ(F): 1.23 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 704 5 %
Rwork0.2293 --
obs0.2313 7701 99.16 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.572 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1-12.2041 Å20 Å20 Å2
2--2.9256 Å20 Å2
3----15.1297 Å2
Refinement stepCycle: LAST / Resolution: 2.34→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 1 30 1227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021219
X-RAY DIFFRACTIONf_angle_d0.5431654
X-RAY DIFFRACTIONf_dihedral_angle_d12.003430
X-RAY DIFFRACTIONf_chiral_restr0.032189
X-RAY DIFFRACTIONf_plane_restr0.002218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3401-2.52080.29791430.30972637X-RAY DIFFRACTION99
2.5208-2.77440.34991380.28062654X-RAY DIFFRACTION99
2.7744-3.17580.34091450.27372683X-RAY DIFFRACTION100
3.1758-4.00080.24241450.23162655X-RAY DIFFRACTION99
4.0008-46.50920.23741330.18222667X-RAY DIFFRACTION99
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)
16.42391.0136-3.17283.2276-3.52176.5413-0.35230.7639-0.7711-0.3337-0.4885-0.04520.911-0.25580.66150.7265-0.01550.05920.368-0.04240.3611-23.3084-10.5695-10.9951
25.2124-0.58134.11020.2003-0.08687.9945-0.14090.4216-0.14090.5122-0.16710.22710.19230.97060.22850.79890.00360.08120.66940.08310.4605-17.2121-4.7556-16.6634
33.24340.9731-2.21558.59572.81932.98630.36460.21050.02621.2123-0.50230.5006-0.0702-2.37510.03010.4846-0.1264-0.02060.6268-0.00960.4529-26.65-5.9763-6.6302
42.8612-2.10550.38356.9895.45486.48140.384-0.0462-0.0466-0.1912-0.3724-0.1227-0.49820.7810.00060.412-0.06930.00830.41180.11220.3048-14.7659-2.2383-6.0631
56.71380.5246-0.04749.7678-5.37933.29330.0439-0.81490.3520.3480.51330.48180.2254-1.2731-0.57190.52160.0064-0.00360.69460.01320.4731-23.0497-1.06281.6686
68.1052-3.80461.1617.24290.86549.7362-0.0987-0.1287-0.17160.79160.43920.65441.40130.3726-0.31370.5068-0.06830.02380.25610.07940.3441-12.6585-3.62145.1056
77.46070.13874.66359.69891.95655.85090.26050.96151.2546-0.5859-0.4521-0.7773-2.18642.22460.18130.8144-0.28650.05670.71620.09240.4476-9.54834.7586-0.1884
87.0851-1.45031.6792.96052.81666.43470.3292-0.72290.35740.2332-0.3910.3723-0.0974-0.36480.09080.4213-0.0750.0640.3213-0.00750.2494-15.04840.49911.6329
94.63851.01111.7449.9381-1.68332.07220.05820.67240.2859-0.3291-0.3063-0.8236-1.58881.5480.05460.4622-0.12660.06260.54250.06760.4031-4.79296.09929.0978
107.1793-1.13992.64024.54751.20325.9397-0.2323-1.07740.09140.50780.2440.3685-0.0913-0.67460.040.4976-0.09390.10030.4442-0.02470.3198-11.56220.952620.1292
118.506-1.33192.64643.3353-0.27961.7851-0.5685-0.5071-0.74932.34590.0215-0.49350.43610.30660.5580.922-0.1680.01710.53120.01310.3565-1.2526.052319.6684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 12 THROUGH 24 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 25 THROUGH 35 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 36 THROUGH 49 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 50 THROUGH 68 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 69 THROUGH 82 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 83 THROUGH 92 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 93 THROUGH 101 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 102 THROUGH 125 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 126 THROUGH 134 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 135 THROUGH 158 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 159 THROUGH 170 )

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