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- PDB-5hab: Crystal structure of mpy-RNase J (mutant H84A), an archaeal RNase... -

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Basic information

Entry
Database: PDB / ID: 5hab
TitleCrystal structure of mpy-RNase J (mutant H84A), an archaeal RNase J from Methanolobus psychrophilus R15, complex with RNA
Components
  • RNA (5'-R(P*AP*AP*AP*AP*A)-3')
  • Ribonuclease J
KeywordsHYDROLASE / exoribonuclease / beta-CASP / MBL / RNase J
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA catabolic process / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribonuclease J, archaea / Ribonuclease J / Ribonuclease J, domain 2 / Beta-lactamase superfamily domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
RNA / Ribonuclease J
Similarity search - Component
Biological speciesMethanolobus psychrophilus R15 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, D.F. / Feng, N.
CitationJournal: To Be Published
Title: Molecular insights into catalysis and processive exonucleolytic mechanisms of prokaryotic RNase J revealing striking parallels with that of eukaryotic Xrn1
Authors: Zheng, X. / Feng, N. / Li, D.F. / Li, J. / Dong, X.Z.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease J
B: Ribonuclease J
C: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
D: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,29313
Polymers107,4294
Non-polymers8659
Water5,080282
1
A: Ribonuclease J
B: Ribonuclease J
C: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
D: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
hetero molecules

A: Ribonuclease J
B: Ribonuclease J
C: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
D: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,58726
Polymers214,8588
Non-polymers1,72918
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area22600 Å2
ΔGint-322 kcal/mol
Surface area67530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.680, 169.680, 167.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-725-

HOH

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Components

#1: Protein Ribonuclease J / RNase J


Mass: 52113.383 Da / Num. of mol.: 2 / Fragment: UNP residues 2-448 / Mutation: H84A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanolobus psychrophilus R15 (archaea)
Gene: rnj, Mpsy_0886 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: K4MAF9, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*A)-3')


Mass: 1601.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8M ammonium sulfate, 3% glycerol / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å
DetectorType: PHILLIPS / Detector: PIXEL / Date: May 18, 2015
RadiationMonochromator: doubel crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.3→84.84 Å / Num. obs: 63078 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 13.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXDEV_1980refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→55.21 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 3119 4.95 %
Rwork0.206 --
obs0.208 63052 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→55.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7142 222 45 282 7691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057560
X-RAY DIFFRACTIONf_angle_d0.93710291
X-RAY DIFFRACTIONf_dihedral_angle_d14.1272822
X-RAY DIFFRACTIONf_chiral_restr0.0431178
X-RAY DIFFRACTIONf_plane_restr0.0041293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33590.36061340.29692696X-RAY DIFFRACTION100
2.3359-2.37420.32761370.27552678X-RAY DIFFRACTION100
2.3742-2.41520.31531290.27552706X-RAY DIFFRACTION100
2.4152-2.45910.33461340.26822706X-RAY DIFFRACTION100
2.4591-2.50640.32671120.26422730X-RAY DIFFRACTION100
2.5064-2.55760.30991340.24512694X-RAY DIFFRACTION100
2.5576-2.61320.27371270.24192709X-RAY DIFFRACTION100
2.6132-2.67390.31581410.25522684X-RAY DIFFRACTION100
2.6739-2.74080.30371540.25492704X-RAY DIFFRACTION100
2.7408-2.81490.31151250.25692699X-RAY DIFFRACTION100
2.8149-2.89770.2961520.24112706X-RAY DIFFRACTION100
2.8977-2.99130.30021570.23782699X-RAY DIFFRACTION100
2.9913-3.09820.29141420.22342710X-RAY DIFFRACTION100
3.0982-3.22220.27651440.22232714X-RAY DIFFRACTION100
3.2222-3.36880.22571560.21312686X-RAY DIFFRACTION100
3.3688-3.54640.25981440.20662740X-RAY DIFFRACTION100
3.5464-3.76860.20841550.19362713X-RAY DIFFRACTION99
3.7686-4.05950.22191540.18212728X-RAY DIFFRACTION99
4.0595-4.46780.21141440.16592755X-RAY DIFFRACTION99
4.4678-5.11390.1681350.15552767X-RAY DIFFRACTION99
5.1139-6.44140.21791420.18882797X-RAY DIFFRACTION99
6.4414-55.22170.19461670.18732912X-RAY DIFFRACTION97

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