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- PDB-5fzs: Designed TPR Protein M4N delta C (CF II) -

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Basic information

Entry
Database: PDB / ID: 5fzs
TitleDesigned TPR Protein M4N delta C (CF II)
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: 1.652 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

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Assembly

Deposited unit
A: DESIGNED TPR PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,8321
Polymers11,8321
Non-polymers00
Water81145
1
A: DESIGNED TPR PROTEIN

A: DESIGNED TPR PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,6642
Polymers23,6642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area1870 Å2
ΔGint-19.2 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.752, 64.752, 86.833
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein DESIGNED TPR PROTEIN


Mass: 11831.779 Da / Num. of mol.: 1
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.: 45 / 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: 43 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→34.3 Å / Num. obs: 13476 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9.21 % / Biso Wilson estimate: 25.17 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.6
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 9.44 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.28 / % possible all: 99

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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: 1.652→34.33 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 944 7 %
Rwork0.1982 --
obs0.1997 13475 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.652→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 0 45 832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006813
X-RAY DIFFRACTIONf_angle_d0.8831096
X-RAY DIFFRACTIONf_dihedral_angle_d11.16318
X-RAY DIFFRACTIONf_chiral_restr0.039135
X-RAY DIFFRACTIONf_plane_restr0.004138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6516-1.73870.28731290.25481712X-RAY DIFFRACTION99
1.7387-1.84760.26991330.23331765X-RAY DIFFRACTION100
1.8476-1.99030.20281310.20411741X-RAY DIFFRACTION100
1.9903-2.19050.23681330.1981765X-RAY DIFFRACTION100
2.1905-2.50740.22881350.17921792X-RAY DIFFRACTION100
2.5074-3.15870.19661360.20141815X-RAY DIFFRACTION100
3.1587-34.33720.21561470.19421941X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 15.9045 Å / Origin y: 19.1758 Å / Origin z: 20.5453 Å
111213212223313233
T0.1459 Å20.0321 Å20.0083 Å2-0.1042 Å20.0029 Å2--0.2886 Å2
L0.3995 °20.5702 °20.4427 °2-1.6176 °20.8202 °2--5.1742 °2
S-0.0316 Å °-0.0327 Å °-0.0249 Å °0.1165 Å °0.0544 Å °-0.019 Å °0.0121 Å °0.0581 Å °-0.028 Å °
Refinement TLS groupSelection details: (CHAIN A)

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