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- PDB-5orq: Crystal structure of designed cPPR-Telo1 in complex with ssDNA -

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Basic information

Entry
Database: PDB / ID: 5orq
TitleCrystal structure of designed cPPR-Telo1 in complex with ssDNA
Components
  • DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
  • cPPR-Telo1
KeywordsDE NOVO PROTEIN / designer nucleic acid-binding proteins / pentatricopeptide repeat / telomerase
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSpahr, H. / Rackham, O.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research CouncilFT0991008, FT0991113, DP140104111 Australia
National Health and Medical Research CouncilAPP1058442, APP1045677 Australia
Cancer Council Western Australia Australia
CitationJournal: Nat Commun / Year: 2018
Title: Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins.
Authors: Spahr, H. / Chia, T. / Lingford, J.P. / Siira, S.J. / Cohen, S.B. / Filipovska, A. / Rackham, O.
History
DepositionAug 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: cPPR-Telo1
B: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)43,3232
Polymers43,3232
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-2 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.831, 114.831, 83.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein cPPR-Telo1


Mass: 40207.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
#2: DNA chain DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Mass: 3115.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 100mM Sodium acetate pH 4.6, 20mM calcium chloride, and 22% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.93→47.32 Å / Num. obs: 42266 / % possible obs: 99.4 % / Redundancy: 27.1 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.014 / Rrim(I) all: 0.074 / Net I/σ(I): 29.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.93-228.72.02440840.7010.382.05999.4
7.48-47.3219.80.0598460.9980.0150.06199.5

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→27.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2011 4.91 %RANDOM
Rwork0.189 ---
obs0.191 40921 99.3 %-
Displacement parametersBiso max: 141.44 Å2 / Biso mean: 29.9 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.2316 Å20 Å20 Å2
2--0.2316 Å20 Å2
3----0.4631 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.95→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 210 0 377 3372
Biso mean---41.31 -
Num. residues----374
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1087SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes404HARMONIC5
X-RAY DIFFRACTIONt_it3050HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion402SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3865SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3050HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4152HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion17.37
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2783 156 5.22 %
Rwork0.2208 2831 -
all0.2237 2987 -
obs--99.5 %
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)
10.97760.748-0.03132.7439-0.0060.2805-0.0774-0.08020.10580.01190.12460.0019-0.03540.0459-0.0472-0.12340.0093-0.0238-0.014-0.0552-0.178610.335223.234817.0451
200.8943-0.51191.69670.00090-0.0457-0.110.12040.07040.09360.083-0.0260.1528-0.0479-0.0058-0.0411-0.01090.00430.03250.02236.076620.165218.6372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 367
2X-RAY DIFFRACTION2{ B|* }B1 - 10

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