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- PDB-4xwt: Crystal structure of RNase J complexed with UMP -

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Basic information

Entry
Database: PDB / ID: 4xwt
TitleCrystal structure of RNase J complexed with UMP
ComponentsDR2417
KeywordsRNA BINDING PROTEIN / ribonuclease / two-metal-ion / dimerization / manganese / Deinococcus radiodurans
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J / Ribonuclease J, domain 2 / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily ...Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J / Ribonuclease J, domain 2 / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Ubiquitin-like (UB roll) / 4-Layer Sandwich / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-5'-MONOPHOSPHATE / Ribonuclease J
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.003 Å
AuthorsLu, M. / Zhang, H. / Xu, Q. / Hua, Y. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China2015CB910600 China
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J
Authors: Zhao, Y. / Lu, M. / Zhang, H. / Hu, J. / Zhou, C. / Xu, Q. / Shah, A.M.U.H. / Xu, H. / Wang, L. / Hua, Y.
History
DepositionJan 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DR2417
B: DR2417
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,60712
Polymers123,4032
Non-polymers1,20410
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-195 kcal/mol
Surface area42220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.590, 87.760, 253.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DR2417


Mass: 61701.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rossetta / References: UniProt: H9CZL7

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Non-polymers , 5 types, 332 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000, MnCl2, MES

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 98253 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 33.99 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.072 / Χ2: 1.042 / Net I/σ(I): 16.09 / Num. measured all: 588280
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.060.8310.6573.2542663731571770.71698.1
2.06-2.110.8960.4934.2444143722572090.53799.8
2.11-2.170.9290.4115.1142482695869460.44799.8
2.17-2.240.9590.3236.2141590680567860.35299.7
2.24-2.310.9660.2657.4440236660165820.28999.7
2.31-2.390.9780.2178.7439149637663600.23799.7
2.39-2.480.9850.17210.6837527614761230.18899.6
2.48-2.590.9890.14112.6836003594559100.15499.4
2.59-2.70.9910.11614.7834363570356660.12699.4
2.7-2.830.9940.09417.5632601546854040.10398.8
2.83-2.990.9960.07521.0230553519251130.08398.5
2.99-3.170.9960.06224.7428396493948210.06897.6
3.17-3.390.9970.05228.3226334464445040.05797
3.39-3.660.9970.04730.7824042433141930.05296.8
3.66-4.010.9980.04133.2521752401638570.04596
4.01-4.480.9980.03835.8420639364734790.04195.4
4.48-5.170.9980.03436.3117806324930590.03894.2
5.17-6.330.9980.03336.2915211275725970.03794.2
6.33-8.960.9980.03435.410204218618650.03785.3
8.960.9970.03731.16258612916020.04146.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata reduction
PDB_EXTRACT3.15data extraction
Cootmodel building
XDSdata processing
RefinementResolution: 2.003→29.473 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 4898 4.99 %
Rwork0.2002 --
obs0.2019 98248 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.003→29.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8288 0 60 322 8670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088587
X-RAY DIFFRACTIONf_angle_d1.12111698
X-RAY DIFFRACTIONf_dihedral_angle_d16.233168
X-RAY DIFFRACTIONf_chiral_restr0.0441339
X-RAY DIFFRACTIONf_plane_restr0.0051546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0034-2.02610.31761480.28323038X-RAY DIFFRACTION97
2.0261-2.050.3271630.27763128X-RAY DIFFRACTION99
2.05-2.07490.31541640.26623185X-RAY DIFFRACTION100
2.0749-2.10120.28041690.25463099X-RAY DIFFRACTION100
2.1012-2.12880.30151510.25683168X-RAY DIFFRACTION100
2.1288-2.1580.32211540.25773190X-RAY DIFFRACTION100
2.158-2.18880.26741520.25283132X-RAY DIFFRACTION100
2.1888-2.22150.29451680.24713155X-RAY DIFFRACTION99
2.2215-2.25620.28671440.23773149X-RAY DIFFRACTION100
2.2562-2.29320.27321650.24523171X-RAY DIFFRACTION100
2.2932-2.33270.31621630.23653098X-RAY DIFFRACTION100
2.3327-2.37510.28481870.23593214X-RAY DIFFRACTION100
2.3751-2.42070.25521630.23013100X-RAY DIFFRACTION100
2.4207-2.47010.29981630.233174X-RAY DIFFRACTION99
2.4701-2.52380.28371520.22443145X-RAY DIFFRACTION100
2.5238-2.58250.28191580.22313182X-RAY DIFFRACTION99
2.5825-2.6470.25641650.22943152X-RAY DIFFRACTION100
2.647-2.71860.27081700.21883136X-RAY DIFFRACTION99
2.7186-2.79850.27271790.22243121X-RAY DIFFRACTION98
2.7985-2.88870.28341690.22983154X-RAY DIFFRACTION99
2.8887-2.99190.23911700.20713124X-RAY DIFFRACTION99
2.9919-3.11160.25941660.21463117X-RAY DIFFRACTION98
3.1116-3.2530.27111640.19813140X-RAY DIFFRACTION98
3.253-3.42430.22991620.193086X-RAY DIFFRACTION97
3.4243-3.63850.22931560.18753127X-RAY DIFFRACTION97
3.6385-3.91880.18361660.16423087X-RAY DIFFRACTION96
3.9188-4.31210.1661850.15523080X-RAY DIFFRACTION96
4.3121-4.93350.17961800.14743069X-RAY DIFFRACTION94
4.9335-6.20610.19581550.17093113X-RAY DIFFRACTION94
6.2061-29.47610.23421470.21362516X-RAY DIFFRACTION73
Refinement TLS params.Method: refined / Origin x: 1.4293 Å / Origin y: 181.8578 Å / Origin z: 27.3601 Å
111213212223313233
T0.3566 Å2-0.1454 Å2-0.0012 Å2-0.3402 Å2-0.0391 Å2--0.2203 Å2
L0.756 °2-0.2834 °20.1361 °2-1.9878 °2-0.0174 °2--0.4992 °2
S0.0401 Å °-0.0863 Å °-0.0855 Å °0.4065 Å °-0.0088 Å °0.0553 Å °0.0327 Å °-0.0137 Å °-0.026 Å °
Refinement TLS groupSelection details: all

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