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- PDB-5izo: Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the ac... -

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Basic information

Entry
Database: PDB / ID: 5izo
TitleBacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site
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) / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / : / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 ...inorganic pyrophosphatase (n-terminal core) / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / : / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / 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. / 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 25, 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 / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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: 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)150,48716
Polymers149,6674
Non-polymers81912
Water9,422523
1
A: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6224
Polymers37,4171
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6224
Polymers37,4171
Non-polymers2053
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)37,6224
Polymers37,4171
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6224
Polymers37,4171
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.652, 119.644, 124.135
Angle α, β, γ (deg.)90.00, 91.59, 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: plasmid / Details (production host): pET28B-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Star (DE3)
References: UniProt: O34600, Hydrolases; Acting on ester bonds, 3'(2'),5'-bisphosphate nucleotidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
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→47.34 Å / Num. obs: 106608 / % possible obs: 94.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.44
Reflection shellResolution: 1.95→2.02 Å / Mean I/σ(I) obs: 2.18 / % possible all: 80

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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: 5J21

5j21


Resolution: 1.95→47.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.259 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 5032 5 %RANDOM
Rwork0.212 ---
obs0.214 94817 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 41.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0.07 Å2
2---0.14 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9534 0 28 523 10085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0229763
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.96513258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72651231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0324.541425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.414151566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3631544
X-RAY DIFFRACTIONr_chiral_restr0.1360.21499
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217382
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_it1.0471.56165
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71529857
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.02733598
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5324.53401
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 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 308 -
Rwork0.314 5689 -
obs--76.39 %

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