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- PDB-4oxp: X-ray crystal structure of the S1 and 5'-sensor domains of RNase ... -

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Basic information

Entry
Database: PDB / ID: 4oxp
TitleX-ray crystal structure of the S1 and 5'-sensor domains of RNase E from Caulobacter crescentus
ComponentsRibonuclease E
KeywordsHYDROLASE / RNase E / endoribonuclease
Function / homology
Function and homology information


ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding / magnesium ion binding ...ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding / magnesium ion binding / zinc ion binding / cytoplasm
Similarity search - Function
: / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / Ribonuclease E / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E/G family / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsVoss, J.E. / Luisi, B.F.L. / Hardwick, S.W.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome.
Authors: Voss, J.E. / Luisi, B.F. / Hardwick, S.W.
History
DepositionFeb 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)32,9781
Polymers32,9781
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.530, 62.530, 155.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ribonuclease E / RNase E


Mass: 32978.074 Da / Num. of mol.: 1 / Fragment: S1 and 5'-sensor domains (UNP residues 1-270) / Mutation: A172V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: rne, CC_1877 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A749, ribonuclease E
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 10% (v/v) Ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9536 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.1→48.7 Å / Num. obs: 18069 / % possible obs: 97 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.62 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.8

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.1→48.7 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.248 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25434 928 5.1 %RANDOM
Rwork0.21165 ---
obs0.2138 17099 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.02 Å2 / Biso mean: 55.292 Å2 / Biso min: 23.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å20 Å2
2---0.35 Å2-0 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 101 1589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191510
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.311.972050
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6835198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41723.90664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8815238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2011511
X-RAY DIFFRACTIONr_chiral_restr0.2140.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211144
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9173.038798
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.4134.52994
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7353.091712
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.54926.5282411
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 69 -
Rwork0.26 1272 -
obs--97.95 %
Refinement TLS params.Method: refined / Origin x: -4.069 Å / Origin y: 11.819 Å / Origin z: -21.4842 Å
111213212223313233
T0.195 Å2-0.0401 Å2-0.1285 Å2-0.0803 Å20.024 Å2--0.2033 Å2
L1.5336 °2-0.4916 °2-0.1976 °2-2.9568 °2-0.735 °2--2.5125 °2
S-0.0089 Å °-0.0465 Å °-0.0871 Å °0.272 Å °-0.1275 Å °-0.4049 Å °-0.1316 Å °0.4409 Å °0.1364 Å °

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