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- PDB-5fzq: Designed TPR Protein M4N -

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Basic information

Entry
Database: PDB / ID: 5fzq
TitleDesigned TPR Protein M4N
ComponentsDESIGNED TPR PROTEIN
KeywordsUNKNOWN FUNCTION / TETRATRICOPEPTIDE / 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 / SAD / Resolution: 2.148 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,92010
Polymers43,2483
Non-polymers6727
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-114.6 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.230, 92.230, 76.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DESIGNED TPR PROTEIN


Mass: 14415.946 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→35.4 Å / Num. obs: 20560 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.38 % / Biso Wilson estimate: 38.77 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.5
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 4.13 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.54 / % possible all: 97.4

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Processing

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

Resolution: 2.148→35.394 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 31.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 1024 5 %
Rwork0.2267 --
obs0.2286 20483 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.148→35.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 35 28 2382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032359
X-RAY DIFFRACTIONf_angle_d0.5243188
X-RAY DIFFRACTIONf_dihedral_angle_d12.187870
X-RAY DIFFRACTIONf_chiral_restr0.021395
X-RAY DIFFRACTIONf_plane_restr0.002399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1483-2.26150.3751420.34212692X-RAY DIFFRACTION97
2.2615-2.40320.33951430.2972729X-RAY DIFFRACTION98
2.4032-2.58870.28681450.27362751X-RAY DIFFRACTION98
2.5887-2.84910.30281440.28072780X-RAY DIFFRACTION99
2.8491-3.26110.29841470.25692773X-RAY DIFFRACTION99
3.2611-4.10770.25821490.19972823X-RAY DIFFRACTION99
4.1077-35.39870.21821540.18362911X-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)
10.02371.05150.3412.41510.06451.90590.0672-0.083-0.03030.03990.01750.13270.0763-0.2002-0.06480.24460.01620.02480.440.00060.379835.736627.057819.507
21.57612.1783-0.13912.0484-0.24422.7183-0.1252-0.0175-0.1382-0.17930.0881-0.0410.36260.21170.04650.45110.13510.00340.30530.01310.416850.910117.379420.4148
31.03260.91112.37682.56682.97025.086-0.2087-0.46810.1382-0.24790.1581-0.0117-0.330.00220.05620.5162-0.11440.0230.632-0.03430.395656.992951.87530.3108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ -10:9999)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ -10:9999)
3X-RAY DIFFRACTION3(CHAIN C AND RESSEQ -10:9999)

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