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- PDB-5fzr: Designed TPR Protein M4N delta C (CF I) -

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Basic information

Entry
Database: PDB / ID: 5fzr
TitleDesigned TPR Protein M4N delta C (CF I)
ComponentsDESIGNED TPR PROTEIN
KeywordsUNKNOWN FUNCTION / TETRATRICOPEPTIDE REPEAT
Function / homologyTetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.045 Å
AuthorsAlbrecht, R. / Zhu, H. / Hartmann, M.D.
CitationJournal: Elife / Year: 2016
Title: Origin of a folded repeat protein from an intrinsically disordered ancestor.
Authors: Zhu, H. / Sepulveda, E. / Hartmann, M.D. / Kogenaru, M. / Ursinus, A. / Sulz, E. / Albrecht, R. / Coles, M. / Martin, J. / Lupas, A.N.
History
DepositionMar 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DESIGNED TPR PROTEIN
B: DESIGNED TPR PROTEIN
C: DESIGNED TPR PROTEIN
D: DESIGNED TPR PROTEIN


Theoretical massNumber of molelcules
Total (without water)47,3274
Polymers47,3274
Non-polymers00
Water2,702150
1
A: DESIGNED TPR PROTEIN
B: DESIGNED TPR PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,6642
Polymers23,6642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-18.6 kcal/mol
Surface area11020 Å2
MethodPISA
2
C: DESIGNED TPR PROTEIN
D: DESIGNED TPR PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,6642
Polymers23,6642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-17.5 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.559, 50.858, 83.921
Angle α, β, γ (deg.)90.00, 102.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DESIGNED TPR PROTEIN


Mass: 11831.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.071
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 2.05→38.3 Å / Num. obs: 25655 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 5.58 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.4
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 5.69 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.1 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FZQ

5fzq


Resolution: 2.045→38.252 Å / SU ML: 0.31 / σ(F): 1.36 / Phase error: 34.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 1281 5 %
Rwork0.2175 --
obs0.2199 25569 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.045→38.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 0 150 3299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033165
X-RAY DIFFRACTIONf_angle_d0.564263
X-RAY DIFFRACTIONf_dihedral_angle_d12.461205
X-RAY DIFFRACTIONf_chiral_restr0.022526
X-RAY DIFFRACTIONf_plane_restr0.002544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0451-2.1270.41131360.35062495X-RAY DIFFRACTION92
2.127-2.22380.34281390.28662683X-RAY DIFFRACTION98
2.2238-2.3410.3841390.27152672X-RAY DIFFRACTION99
2.341-2.48760.31381400.25112682X-RAY DIFFRACTION98
2.4876-2.67970.30241440.25062709X-RAY DIFFRACTION99
2.6797-2.94920.28961430.24942725X-RAY DIFFRACTION99
2.9492-3.37580.28361470.25142752X-RAY DIFFRACTION99
3.3758-4.25220.25611440.18742746X-RAY DIFFRACTION100
4.2522-38.25820.19191490.17032824X-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)
13.08451.76163.44692.2012.00187.8109-0.0445-0.3807-0.0535-0.02240.0085-0.0764-0.1849-0.06360.02030.2210.04840.04180.38070.04990.26062.37897.199318.8511
22.8046-0.98431.2691.9619-0.25717.1780.1495-0.433-0.21450.130.32370.19190.6076-0.1206-0.4240.3478-0.03960.01140.38590.05290.3432-6.432-7.577122.7989
35.26010.24435.3562-0.15210.50275.82010.066-0.8239-0.43040.12040.23980.1065-0.0428-0.8764-0.30170.41320.01090.05820.39970.15920.39192.7202-4.906362.8178
42.792-0.81251.47431.094-0.95069.3521-0.15130.36890.158-0.03360.07560.0444-0.2845-0.21490.06650.3526-0.1075-0.00650.30630.05590.288715.64594.678756.9152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)
3X-RAY DIFFRACTION3(CHAIN C)
4X-RAY DIFFRACTION4(CHAIN D)

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