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- PDB-5yjj: Crystal structure of PNPase from Staphylococcus epidermidis -

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Basic information

Entry
Database: PDB / ID: 5yjj
TitleCrystal structure of PNPase from Staphylococcus epidermidis
ComponentsPolyribonucleotide nucleotidyltransferase
KeywordsCYTOSOLIC PROTEIN / polynucleotidyl phosphorylase / RNA degradation / Polyadenylation
Function / homology
Function and homology information


polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / mRNA catabolic process / RNA processing / magnesium ion binding / RNA binding / cytoplasm
Similarity search - Function
Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase, RNA binding domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 ...Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase, RNA binding domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / KH domain / RNA-binding domain, S1 / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K Homology domain / K homology RNA-binding domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
PHOSPHATE ION / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRaj, R. / Gopal, B.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Characterization of Staphylococcus epidermidis Polynucleotide phosphorylase and its interactions with ribonucleases RNase J1 and RNase J2.
Authors: Raj, R. / Mitra, S. / Gopal, B.
History
DepositionOct 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Polyribonucleotide nucleotidyltransferase
B: Polyribonucleotide nucleotidyltransferase
C: Polyribonucleotide nucleotidyltransferase
D: Polyribonucleotide nucleotidyltransferase
E: Polyribonucleotide nucleotidyltransferase
F: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,32318
Polymers473,6076
Non-polymers71612
Water29,1661619
1
A: Polyribonucleotide nucleotidyltransferase
B: Polyribonucleotide nucleotidyltransferase
C: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,1619
Polymers236,8043
Non-polymers3586
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-97 kcal/mol
Surface area50280 Å2
MethodPISA
2
D: Polyribonucleotide nucleotidyltransferase
E: Polyribonucleotide nucleotidyltransferase
F: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,1619
Polymers236,8043
Non-polymers3586
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-100 kcal/mol
Surface area49710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.190, 93.160, 143.150
Angle α, β, γ (deg.)73.54, 87.61, 60.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / PNPase


Mass: 78934.500 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 12228) (bacteria)
Strain: ATCC 12228 / Gene: pnp, pnpA, SE_0951 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8CST1, polyribonucleotide nucleotidyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1619 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.3 / Details: 0.2M Potassium formate, 20% PEG 3350, pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.2→75.03 Å / Num. obs: 196762 / % possible obs: 97.6 % / Redundancy: 4.5 % / Net I/σ(I): 8.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CDI

3cdi


Resolution: 2.2→73.04 Å / Cross valid method: FREE R-VALUE / σ(F): 19.21 / Phase error: 40.81
RfactorNum. reflection% reflection
Rfree0.259 10175 5.17 %
Rwork0.237 --
obs0.3 196757 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→73.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19814 0 36 1619 21469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00620155
X-RAY DIFFRACTIONf_angle_d0.85527268
X-RAY DIFFRACTIONf_dihedral_angle_d17.3817351
X-RAY DIFFRACTIONf_chiral_restr0.0693181
X-RAY DIFFRACTIONf_plane_restr0.0043556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2380.44064740.40929243X-RAY DIFFRACTION92
2.238-2.27870.46424670.40139319X-RAY DIFFRACTION92
2.2787-2.32250.41914520.39599285X-RAY DIFFRACTION92
2.3225-2.36990.4565230.39679243X-RAY DIFFRACTION92
2.3699-2.42150.42314990.39969252X-RAY DIFFRACTION92
2.4215-2.47780.45255030.39699300X-RAY DIFFRACTION92
2.4778-2.53980.40664620.3939324X-RAY DIFFRACTION93
2.5398-2.60840.42484470.39169353X-RAY DIFFRACTION93
2.6084-2.68520.38274740.38269387X-RAY DIFFRACTION93
2.6852-2.77190.3924540.36539347X-RAY DIFFRACTION93
2.7719-2.87090.3984790.35829344X-RAY DIFFRACTION93
2.8709-2.98590.37534530.35479432X-RAY DIFFRACTION93
2.9859-3.12180.35284830.31539398X-RAY DIFFRACTION93
3.1218-3.28630.31815690.29579290X-RAY DIFFRACTION92
3.2863-3.49220.28875280.26659335X-RAY DIFFRACTION93
3.4922-3.76180.28914960.25259434X-RAY DIFFRACTION93
3.7618-4.14030.25355520.23569300X-RAY DIFFRACTION93
4.1403-4.73910.25414680.22429489X-RAY DIFFRACTION94
4.7391-5.96980.2714570.25589465X-RAY DIFFRACTION94
5.9698-57.44550.32635550.29859395X-RAY DIFFRACTION93

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