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- PDB-5ipp: Structure of Bacillus NanoRNase A active site mutant bound to a m... -

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Basic information

Entry
Database: PDB / ID: 5ipp
TitleStructure of Bacillus NanoRNase A active site mutant bound to a mononucleotide
ComponentsBifunctional oligoribonuclease and PAP phosphatase NrnA
KeywordsHYDROLASE / nanoRNA / RNA degradation / exonuclease / RNase / abortive transcripts / pAp phosphatase
Function / homology
Function and homology information


3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / exonuclease activity / Hydrolases; Acting on ester bonds / nucleic acid binding
Similarity search - Function
Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll ...Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Bifunctional oligoribonuclease and PAP phosphatase NrnA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSchmier, B.J. / Nelersa, C.M. / Malhotra, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM69972 United States
CitationJournal: Sci Rep / Year: 2017
Title: Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA.
Authors: Schmier, B.J. / Nelersa, C.M. / Malhotra, A.
History
DepositionMar 9, 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
Revision 2.0Jul 10, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_keywords / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_keywords.text / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,3626
Polymers149,6674
Non-polymers6942
Water13,691760
1
A: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7642
Polymers37,4171
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional oligoribonuclease and PAP phosphatase NrnA


Theoretical massNumber of molelcules
Total (without water)37,4171
Polymers37,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7642
Polymers37,4171
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional oligoribonuclease and PAP phosphatase NrnA


Theoretical massNumber of molelcules
Total (without water)37,4171
Polymers37,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.031, 125.193, 116.818
Angle α, β, γ (deg.)90.00, 90.20, 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: 37416.793 Da / Num. of mol.: 4 / Mutation: H103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: nrnA, ytqI, BSU29250 / Plasmid: pET28B-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Star (DE3)
References: UniProt: O34600, 3'(2'),5'-bisphosphate nucleotidase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 760 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: PEG MME 2000, sodium acetate, ammonium acetate, glycerol
PH range: 4.5-5.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→46.82 Å / Num. obs: 98753 / % possible obs: 97.58 % / Redundancy: 3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.44
Reflection shellResolution: 1.95→2 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.82 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.6 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.156 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23761 5247 5 %RANDOM
Rwork0.18552 ---
obs0.18812 98753 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 23.894 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.02 Å2
2---0.04 Å20 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.95→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9919 0 46 760 10725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02210019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.96713610
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9251257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4224.364440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.516151635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3031549
X-RAY DIFFRACTIONr_chiral_restr0.1440.21533
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217587
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_it1.1711.56247
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.957210043
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.33733772
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1514.53567
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 325 -
Rwork0.262 6218 -
obs--83.46 %

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