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- PDB-5orm: Crystal structure of designed cPPR-Telo1 -

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Basic information

Entry
Database: PDB / ID: 5orm
TitleCrystal structure of designed cPPR-Telo1
ComponentscPPR-Telo1
KeywordsDE NOVO PROTEIN / designer nucleic acid-binding proteins / pentatricopeptide repeat / telomerase
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsSpahr, H. / Rackham, O.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research CouncilFT0991008, FT0991113, DP140104111 Australia
the 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cPPR-Telo1


Theoretical massNumber of molelcules
Total (without water)38,7581
Polymers38,7581
Non-polymers00
Water15,133840
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.380, 87.100, 91.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cPPR-Telo1


Mass: 38758.074 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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

CrystalMosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 100mM sodium acetate pH 4.6, 20mM calcium chloride, and 40% 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: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.08→86.4 Å / Num. obs: 40891 / % possible obs: 96.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 23.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.035 / Rrim(I) all: 0.117 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.08-2.134.91.41124150.6740.6951.58179.8
9.3-86.410.40.0915620.9950.0290.09699.9

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→19.7 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2061 5.04 %RANDOM
Rwork0.24 ---
obs0.243 40891 97 %-
Displacement parametersBiso max: 103.7 Å2 / Biso mean: 30.58 Å2 / Biso min: 6.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.3739 Å20 Å20 Å2
2--2.4569 Å20 Å2
3----1.083 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.08→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 0 840 3523
Biso mean---44.88 -
Num. residues----350
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1002SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes379HARMONIC5
X-RAY DIFFRACTIONt_it2712HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion357SEMIHARMONIC5
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_contact3673SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2712HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3650HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion18.17
LS refinement shellResolution: 2.08→2.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2407 117 4.8 %
Rwork0.2502 2319 -
all0.2497 2436 -
obs--79.24 %
Refinement TLS params.Method: refined / Origin x: -17.3126 Å / Origin y: 87.1274 Å / Origin z: 15.641 Å
111213212223313233
T0.0178 Å2-0.0071 Å20.0103 Å2-0.0344 Å2-0.0145 Å2---0.0304 Å2
L0.0354 °2-0.0754 °20.2578 °2-0 °2-0.1003 °2--0.2148 °2
S-0.1374 Å °-0.0156 Å °-0.0394 Å °0.0332 Å °0.0764 Å °-0.0568 Å °0.0329 Å °0.0189 Å °0.0611 Å °
Refinement TLS groupSelection details: { A|* }

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