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- PDB-5j21: Structure of Bacillus NanoRNase A (WT) -

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Basic information

Entry
Database: PDB / ID: 5j21
TitleStructure of Bacillus NanoRNase A (WT)
ComponentsBifunctional oligoribonuclease and PAP phosphatase NrnA
KeywordsHYDROLASE / nanoRNA / RNA degradation / exonuclease / RNase / B. subtilis / abortive transcripts / pAp phosphatase
Function / homology
Function and homology information


3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds
Similarity search - Function
inorganic pyrophosphatase (n-terminal core) / : / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Bifunctional oligoribonuclease and PAP phosphatase NrnA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchmier, B.J. / Malhotra, A. / Nelersa, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM69972 United States
Citation
Journal: Sci Rep / Year: 2017
Title: Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA.
Authors: Schmier, B.J. / Nelersa, C.M. / Malhotra, A.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2011
Title: Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation.
Authors: Nelersa, C.M. / Schmier, B.J. / Malhotra, A.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional oligoribonuclease and PAP phosphatase NrnA
B: Bifunctional oligoribonuclease and PAP phosphatase NrnA
C: Bifunctional oligoribonuclease and PAP phosphatase NrnA
D: Bifunctional oligoribonuclease and PAP phosphatase NrnA


Theoretical massNumber of molelcules
Total (without water)149,9354
Polymers149,9354
Non-polymers00
Water12,322684
1
A: Bifunctional oligoribonuclease and PAP phosphatase NrnA


Theoretical massNumber of molelcules
Total (without water)37,4841
Polymers37,4841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional oligoribonuclease and PAP phosphatase NrnA


Theoretical massNumber of molelcules
Total (without water)37,4841
Polymers37,4841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional oligoribonuclease and PAP phosphatase NrnA


Theoretical massNumber of molelcules
Total (without water)37,4841
Polymers37,4841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional oligoribonuclease and PAP phosphatase NrnA


Theoretical massNumber of molelcules
Total (without water)37,4841
Polymers37,4841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.616, 121.250, 123.388
Angle α, β, γ (deg.)90.00, 91.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bifunctional oligoribonuclease and PAP phosphatase NrnA / 3'(2') / 5'-bisphosphate nucleotidase / 3'-phosphoadenosine 5'-phosphate phosphatase / PAP ...3'(2') / 5'-bisphosphate nucleotidase / 3'-phosphoadenosine 5'-phosphate phosphatase / PAP phosphatase / nanoRNase


Mass: 37483.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: nrnA, ytqI, BSU29250 / Plasmid: pET28a-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Star
References: UniProt: O34600, 3'(2'),5'-bisphosphate nucleotidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: PEG MME 2000, sodium acetate, ammonium acetate, glycerol
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→46.44 Å / Num. obs: 93522 / % possible obs: 98.3 % / Redundancy: 5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 35.19
Reflection shellResolution: 2→2.03 Å / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DEV

3dev


Resolution: 2→46.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.834 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4943 5 %RANDOM
Rwork0.18 ---
obs0.183 93522 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 32.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.01 Å2
2---0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9748 0 0 685 10433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0229950
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0721.96113513
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23151253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04824.305439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.697151627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3361549
X-RAY DIFFRACTIONr_chiral_restr0.1720.21520
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217549
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_it1.3211.56233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.247210004
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.78233717
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8184.53509
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→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 346 -
Rwork0.253 6312 -
obs--90.22 %

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