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- PDB-4xww: Crystal structure of RNase J complexed with RNA -

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Basic information

Entry
Database: PDB / ID: 4xww
TitleCrystal structure of RNase J complexed with RNA
Components
  • DR2417
  • RNA (5'-D(UP*UP*UP*UP*UP*UP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / ribonuclease / two-metal-ion / dimerization / manganese / Deinococcus radiodurans / RNA BINDING PROTEIN-RNA complex
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
: / RNA / Ribonuclease J
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 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
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DR2417
B: DR2417
D: RNA (5'-D(UP*UP*UP*UP*UP*UP*U)-3')
E: RNA (5'-D(UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,15512
Polymers127,5994
Non-polymers5568
Water13,673759
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-251 kcal/mol
Surface area41620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.120, 87.860, 249.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / RNA chain , 2 types, 4 molecules ABDE

#1: Protein DR2417


Mass: 61701.379 Da / Num. of mol.: 2 / Mutation: D175A
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
#2: RNA chain RNA (5'-D(UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2098.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 767 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 293 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: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 158299 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 23.66 Å2 / Rmerge F obs: 0.992 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.112 / Χ2: 0.971 / Net I/σ(I): 10.69 / Num. measured all: 936565
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
1.7-1.740.6470.6971.92390741194395360.79679.8
1.74-1.790.8390.572.926173611614111700.6396.2
1.79-1.840.910.4444.036972911323112430.48599.3
1.84-1.90.940.345.136735110944108730.37299.4
1.9-1.960.9590.2616.436577010681106240.28699.5
1.96-2.030.970.2048.056324210308102460.22499.4
2.03-2.110.9710.1699.5561057994898950.18699.5
2.11-2.190.9770.14710.8458685959195560.16299.6
2.19-2.290.9770.13212.0256135922091680.14599.4
2.29-2.40.980.1213.0753463884687840.13299.3
2.4-2.530.980.11114.1350496836982910.12399.1
2.53-2.690.9810.10415.1747857801179000.11598.6
2.69-2.870.9830.09816.0744667745673520.10898.6
2.87-3.10.9850.09217.1641742701269470.10199.1
3.1-3.40.9850.08918.0738322647664010.09898.8
3.4-3.80.9850.08718.5434764587758260.09699.1
3.8-4.390.9870.08518.8330441521651760.09499.2
4.39-5.370.9870.08218.7425308445343910.0998.6
5.37-7.60.9870.08218.5419970350234460.0998.4
7.60.9780.08116.426756204214740.09172.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata reduction
PDB_EXTRACT3.15data extraction
Cootmodel building
XDSphasing
RefinementResolution: 1.7→29.591 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 7889 5.02 %
Rwork0.1949 149260 -
obs0.196 157149 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.79 Å2 / Biso mean: 37.8393 Å2 / Biso min: 12.98 Å2
Refinement stepCycle: final / Resolution: 1.7→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8293 242 18 759 9312
Biso mean--37.55 40.03 -
Num. residues----1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078800
X-RAY DIFFRACTIONf_angle_d1.10912029
X-RAY DIFFRACTIONf_chiral_restr0.0491392
X-RAY DIFFRACTIONf_plane_restr0.0061554
X-RAY DIFFRACTIONf_dihedral_angle_d15.7473282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.71940.36091850.30483565375070
1.7194-1.73970.30392450.27234219446484
1.7397-1.76090.31792140.25544624483889
1.7609-1.78320.28822820.25144881516397
1.7832-1.80660.25542640.245057532199
1.8066-1.83140.2472510.24075062531399
1.8314-1.85750.29772640.24165048531299
1.8575-1.88530.26292180.22935085530399
1.8853-1.91470.25782790.22695098537799
1.9147-1.94610.23442730.2225035530899
1.9461-1.97960.26022900.22065090538099
1.9796-2.01560.25742360.211650925328100
2.0156-2.05440.24152630.21345060532399
2.0544-2.09630.21652890.20695093538299
2.0963-2.14190.25542880.20565030531899
2.1419-2.19170.24492690.20755079534899
2.1917-2.24650.2182910.19695080537199
2.2465-2.30720.21452450.20745095534099
2.3072-2.37510.2252640.20365066533099
2.3751-2.45170.23232830.19835054533798
2.4517-2.53930.21822880.20255038532699
2.5393-2.64090.21892730.20395056532998
2.6409-2.7610.24252810.19835060534198
2.761-2.90640.21942720.19865100537298
2.9064-3.08840.20482760.19195078535499
3.0884-3.32650.19822820.18215097537998
3.3265-3.66070.18032500.17235177542799
3.6607-4.18920.18372720.16285189546199
4.1892-5.2730.16842450.15645216546198
5.273-29.5950.22932570.21114836509388
Refinement TLS params.Method: refined / Origin x: 1.7308 Å / Origin y: 97.3975 Å / Origin z: 26.5299 Å
111213212223313233
T0.239 Å2-0.0431 Å2-0.016 Å2-0.2106 Å20.0235 Å2--0.0787 Å2
L0.6894 °20.1281 °20.1285 °2-1.7682 °20.0429 °2--0.3762 °2
S0.0761 Å °-0.1348 Å °-0.0707 Å °0.4552 Å °-0.0406 Å °-0.0305 Å °0.0577 Å °-0.0028 Å °-0.0314 Å °
Refinement TLS groupSelection details: all

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