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- PDB-6u7v: xRRM structure of spPof8 -

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Basic information

Entry
Database: PDB / ID: 6u7v
TitlexRRM structure of spPof8
ComponentsProtein pof8
KeywordsGENE REGULATION / Telomere / Telomerase / RNA binding / TER1 / xRRM
Function / homology
Function and homology information


nuclear RNA surveillance / telomerase catalytic core complex assembly / telomerase RNA stabilization / chromosome, telomeric repeat region / telomerase holoenzyme complex / telomerase RNA binding / telomere maintenance via telomerase / chromatin binding / nucleus / cytosol
Similarity search - Function
La-related protein 7 homolog, xRRM domain / xRRM domain / xRRM domain profile. / La protein, xRRM domain / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
NITRATE ION / La-related protein 7 homolog
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.42 Å
AuthorsKim, J.-K. / Hu, X. / Yu, C. / Jun, H.-I. / Liu, J. / Sankaran, B. / Huang, L. / Qiao, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098943 United States
CitationJournal: Cell Rep / Year: 2020
Title: Quality-Control Mechanism for Telomerase RNA Folding in the Cell.
Authors: Hu, X. / Kim, J.K. / Yu, C. / Jun, H.I. / Liu, J. / Sankaran, B. / Huang, L. / Qiao, F.
History
DepositionSep 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein pof8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5512
Polymers15,4891
Non-polymers621
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.672, 57.672, 71.014
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein pof8


Mass: 15489.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: pof8, SPAC17G6.17 / Production host: Escherichia coli (E. coli) / References: UniProt: O13795
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 19-21.5% PEG3350, 50 mM Hepes pH 7.5, 90-110 mM Na Nitrate for Se-Met

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97932, 0.97600, 1.37755
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.9761
31.377551
ReflectionResolution: 1.4→50 Å / Num. obs: 27356 / % possible obs: 99.7 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.015 / Rrim(I) all: 0.043 / Χ2: 1.843 / Net I/σ(I): 23.4 / Num. measured all: 237237
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.428.60.43213530.9260.1560.4591.428100
1.42-1.458.70.3613410.9540.1280.3821.41100
1.45-1.488.70.30913510.9670.110.3281.43100
1.48-1.518.80.24613380.9780.0880.2621.485100
1.51-1.548.80.20713490.9840.0740.221.451100
1.54-1.588.80.17413730.9880.0620.1851.456100
1.58-1.628.80.14313550.9930.0510.1521.525100
1.62-1.668.80.12813480.9940.0450.1361.503100
1.66-1.718.80.10813560.9950.0380.1151.515100
1.71-1.768.90.08713590.9970.0310.0931.507100
1.76-1.838.80.0713800.9990.0250.0741.531100
1.83-1.98.80.05913430.9980.0210.0631.639100
1.9-1.998.80.04913850.9990.0170.0521.675100
1.99-2.098.80.03913630.9990.0140.0421.62799.9
2.09-2.228.80.03513890.9990.0120.0371.631100
2.22-2.398.70.03513640.9990.0120.0372.062100
2.39-2.638.60.04214000.9990.0150.0443.074100
2.63-3.028.50.03513870.9990.0130.0383.06399.9
3.02-3.88.10.023141410.0090.0252.07799.7
3.8-507.90.02814080.9990.0110.033.95594

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.42→40.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.892 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.061
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 1331 5.1 %RANDOM
Rwork0.1699 ---
obs0.1709 24895 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.18 Å2 / Biso mean: 18.903 Å2 / Biso min: 7.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.42→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 4 180 1158
Biso mean--11.28 31.94 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131078
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171004
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.6661464
X-RAY DIFFRACTIONr_angle_other_deg1.4531.5832339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.34920.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41615205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0731511
X-RAY DIFFRACTIONr_chiral_restr0.1140.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021229
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02240
LS refinement shellResolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 99 -
Rwork0.211 1826 -
all-1925 -
obs--99.95 %

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