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- PDB-2ix0: RNase II -

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Basic information

Entry
Database: PDB / ID: 2ix0
TitleRNase II
ComponentsEXORIBONUCLEASE 2
KeywordsHYDROLASE / S1 / RNA / CSD / RNB / NUCLEASE / RNASE II / RNA- BINDING / EXONUCLEASE
Function / homology
Function and homology information


exoribonuclease II / exoribonuclease II activity / mRNA catabolic process / 3'-5' exonuclease activity / 3'-5'-RNA exonuclease activity / RNA binding / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #640 / Ribonuclease II / Ribonuclease B, N-terminal OB domain / Ribonuclease B OB domain / Cold shock domain / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #640 / Ribonuclease II / Ribonuclease B, N-terminal OB domain / Ribonuclease B OB domain / Cold shock domain / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / Cold shock domain / Cold shock protein domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / Exoribonuclease 2
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsFrazao, C. / Mcvey, C.E. / Amblar, M. / Barbas, A. / Vonrhein, C. / Arraiano, C.M. / Carrondo, M.A.
Citation
Journal: Nature / Year: 2006
Title: Unravelling the Dynamics of RNA Degradation by Ribonuclease II and its RNA-Bound Complex
Authors: Frazao, C. / Mcvey, C.E. / Amblar, M. / Barbas, A. / Vonrhein, C. / Arraiano, C.M. / Carrondo, M.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, Purification, Crystallization and Preliminary Diffraction Data Characterization of Escherichia Coli Ribonuclease II (Rnase II)
Authors: Mcvey, C.E. / Amblar, M. / Barbas, A. / Cairrao, F. / Coelho, R. / Romao, C. / Arraiano, C.M. / Carrondo, M.A. / Frazao, C.
#2: Journal: J.Mol.Biol. / Year: 2006
Title: Characterization of the Functional Domains of Escherichia Coli Rnase II.
Authors: Amblar, M. / Barbas, A. / Fialho, A.M. / Arraiano, C.M.
#3: Journal: Mol.Microbiol. / Year: 1993
Title: DNA Sequencing and Expression of the Gene Rnb Encoding Escherichia Coli Ribonuclease II
Authors: Zilhao, R. / Camelo, L. / Arraiano, C.M.
History
DepositionJul 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXORIBONUCLEASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9874
Polymers74,5991
Non-polymers3883
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.836, 125.719, 66.244
Angle α, β, γ (deg.)90.00, 111.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EXORIBONUCLEASE 2 / / RNASE II / EXORIBONUCLEASE II / RIBONUCLEASE II


Mass: 74598.945 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-644
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: C600 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30850, exoribonuclease II
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HIS-TAGGED PROTEIN, WHERE THE FIRST 5 RESIDUES, MFQDN, ARE REPLACED BY ...N-TERMINAL HIS-TAGGED PROTEIN, WHERE THE FIRST 5 RESIDUES, MFQDN, ARE REPLACED BY MGSSHHHHHHSSGLVPRGSHMLED. N- TERMINUS INVISIBLE IN ELECTRON DENSITY.

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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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: VAPOUR DIFFUSION IN SITTING DROPS WITH 1.5 MICRO-L OF PROTEIN SOLUTION, 8-12 MG/ML 3% GLYCEROL 1 MM MGCL2 100 MM KCL AND 100 MM TRIS-HCL PH 8.0, AND 1.5 MICRO-L OF WELL SOLUTION, 22 % PEG ...Details: VAPOUR DIFFUSION IN SITTING DROPS WITH 1.5 MICRO-L OF PROTEIN SOLUTION, 8-12 MG/ML 3% GLYCEROL 1 MM MGCL2 100 MM KCL AND 100 MM TRIS-HCL PH 8.0, AND 1.5 MICRO-L OF WELL SOLUTION, 22 % PEG 4K, 0.6M CA ACETATE AND 0.1M TRIS-HCL PH 8.5, AT 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.975
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.44→43.94 Å / Num. obs: 31569 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.4
Reflection shellResolution: 2.44→2.53 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IX1

2ix1


Resolution: 2.44→62.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 17.3 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.DISOREDERED N-TERMINUS UNTIL RESIDUE 4 AND LOOP BETWEEN REIDUES 30-33 AND 67-70 WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1576 5 %RANDOM
Rwork0.187 ---
obs0.19 29969 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.44→62.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 23 145 5210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225287
X-RAY DIFFRACTIONr_bond_other_d0.0080.024913
X-RAY DIFFRACTIONr_angle_refined_deg2.321.9647162
X-RAY DIFFRACTIONr_angle_other_deg4.412311380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9625638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94223.271269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.78515933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6931558
X-RAY DIFFRACTIONr_chiral_restr0.4150.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025864
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021108
X-RAY DIFFRACTIONr_nbd_refined0.2190.2970
X-RAY DIFFRACTIONr_nbd_other0.2110.24750
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22414
X-RAY DIFFRACTIONr_nbtor_other0.1410.23503
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.43423333
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.70735183
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.98442230
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.48861979
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 88
Rwork0.261 2131
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1231-0.3041-0.02380.8005-0.3082.73840.07250.19720.1394-0.23480.04440.1408-0.0647-0.2799-0.11690.0489-0.0127-0.07560.11880.0058-0.031725.18284.38690.7738
21.0322-0.3815-0.93420.2706-0.14812.72410.0103-0.05710.0731-0.05410.0402-0.03010.1819-0.0299-0.05050.0237-0.02410.00780.08440.00220.063224.17771.005126.649
30.0633-0.1994-0.04481.5620.16640.067-0.2106-0.0559-0.08970.27210.1386-0.0903-0.07590.1390.0720.11170.0203-0.04180.0881-0.01710.08216.364130.552151.7543
41.04780.84970.86431.1280.6391.1697-0.0583-0.1304-0.09650.25380.11930.1656-0.02330.0362-0.0610.10660.09830.0813-0.01660.01950.1168-9.800231.424152.9513
51.63351.19590.33960.87540.24860.07060.3907-0.4945-0.0801-0.594-0.36350.3312-0.28510.0079-0.02730.17720.10720.08230.1130.04040.0949-4.55689.292546.8825
60.23260.30850.3621.31590.14171.2824-0.1052-0.03890.1559-0.3089-0.0690.1658-0.10070.00890.17420.10380.0494-0.0443-0.03480.02190.0896-7.323728.492227.1098
70.19860.6997-0.31273.3767-0.72010.65220.0767-0.01020.0803-0.13530.1453-0.278-0.04140.1446-0.22190.074-0.00290.01020.0718-0.04350.11169.841827.722638.6742
80.43530.12011.11520.64930.33532.8582-0.06520.0244-0.03580.03760.08960.1627-0.13130.2444-0.02440.0016-0.04210.01480.09860.00420.1086-6.3727-2.685426.5952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 45
2X-RAY DIFFRACTION2A46 - 169
3X-RAY DIFFRACTION3A170 - 266
4X-RAY DIFFRACTION4A267 - 359
5X-RAY DIFFRACTION5A360 - 387
6X-RAY DIFFRACTION6A388 - 497
7X-RAY DIFFRACTION7A498 - 548
8X-RAY DIFFRACTION8A549 - 644

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