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- PDB-5mtz: Crystal structure of a long form RNase Z from yeast -

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Basic information

Entry
Database: PDB / ID: 5mtz
TitleCrystal structure of a long form RNase Z from yeast
ComponentsRibonuclease Z
KeywordsHYDROLASE / ZINC-DEPENDENT METAL HYDROLASE / RIBONUCLEASE Z
Function / homology
Function and homology information


: / : / tRNase Z / mitochondrial tRNA 3'-end processing / 3'-tRNA processing endoribonuclease activity / tRNA 3'-end processing / mitochondrion / nucleus / metal ion binding / cytoplasm
Similarity search - Function
tRNase Z endonuclease / tRNase Z endonuclease / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
PHOSPHATE ION / Ribonuclease Z
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.99 Å
AuthorsLi de la Sierra-Gallay, I. / Miao, M. / van Tilbeurgh, H.
Funding support China, France, 2items
OrganizationGrant numberCountry
China Scholarship Council201206180025 China
French Infrastructure for Integrates Structural Biology (FRISBI)ANR-10-INSB-05 France
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The crystal structure of Trz1, the long form RNase Z from yeast.
Authors: Ma, M. / Li de la Sierra-Gallay, I. / Lazar, N. / Pellegrini, O. / Durand, D. / Marchfelder, A. / Condon, C. / van Tilbeurgh, H.
History
DepositionJan 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease Z
B: Ribonuclease Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,4848
Polymers204,0332
Non-polymers4526
Water00
1
A: Ribonuclease Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2424
Polymers102,0161
Non-polymers2263
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2424
Polymers102,0161
Non-polymers2263
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.000, 136.000, 115.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Ribonuclease Z / RNase Z / tRNA 3 endonuclease / tRNase Z


Mass: 102016.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TRZ1, YKR079C / Production host: Escherichia coli DH5[alpha] (bacteria) / Variant (production host): DE3 / References: UniProt: P36159, tRNase Z
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes, pH 7.5, 25% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.99→49.61 Å / Num. obs: 83709 / % possible obs: 99.7 % / Redundancy: 7.8 % / Biso Wilson estimate: 72.1 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.99-3.177.6292.2740.83133040.3812.43798.4
3.17-3.397.6981.3321.54127820.6281.428100
3.39-3.667.7980.7443.01118170.8740.798100
3.66-4.017.7410.4365.45109460.9470.467100
4.01-4.477.7880.249.5598260.9810.257100
4.47-5.167.9040.15413.4587210.990.165100
5.16-6.37.920.16112.8673460.9890.172100
6.3-8.847.9260.10717.6457370.9950.114100
8.84-49.6077.7570.05929.9432300.9970.06399.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata scaling
XDSdata reduction
SHELXCDphasing
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.99→49.61 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.901 / SU B: 23.876 / SU ML: 0.415 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.442
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 2135 5 %RANDOM
Rwork0.1809 ---
obs0.1849 40563 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 198.53 Å2 / Biso mean: 82.768 Å2 / Biso min: 42.24 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å20 Å20 Å2
2---2.09 Å20 Å2
3---4.18 Å2
Refinement stepCycle: final / Resolution: 2.99→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12458 0 14 0 12472
Biso mean--83.16 --
Num. residues----1523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912774
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211583
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.95717269
X-RAY DIFFRACTIONr_angle_other_deg1.014326971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84651517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8924.863658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.589152164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6641556
X-RAY DIFFRACTIONr_chiral_restr0.0880.21886
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214089
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022615
LS refinement shellResolution: 2.99→3.067 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 153 -
Rwork0.387 2913 -
all-3066 -
obs--97.58 %

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