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- PDB-1e3p: tungstate derivative of Streptomyces antibioticus PNPase/GPSI enzyme -

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Basic information

Entry
Database: PDB / ID: 1e3p
Titletungstate derivative of Streptomyces antibioticus PNPase/GPSI enzyme
ComponentsPolyribonucleotide nucleotidyltransferasePolynucleotide phosphorylase
KeywordsPOLYRIBONUCLEOTIDE TRANSFERASE / ATP-GTP DIPHOSPHOTRANSFERASE RNA PROCESSING / RNA DEGRADATION
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
Guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase, RNA binding domain / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily ...Guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase, RNA binding domain / GHMP Kinase, N-terminal domain / 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 S5; domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K Homology domain / K homology RNA-binding domain / Arc Repressor Mutant, subunit A / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSymmons, M.F. / Jones, G.H. / Luisi, B.F.
CitationJournal: Structure / Year: 2000
Title: A Duplicated Fold is the Structural Basis for Polynucleotide Phosphorylase Catalytic Activity, Processivity, and Regulation
Authors: Symmons, M.F. / Jones, G.H. / Luisi, B.F.
History
DepositionJun 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id
Revision 1.4Dec 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,43412
Polymers81,2251
Non-polymers1,20811
Water5,495305
1
A: Polyribonucleotide nucleotidyltransferase
hetero molecules

A: Polyribonucleotide nucleotidyltransferase
hetero molecules

A: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,30236
Polymers243,6763
Non-polymers3,62533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12130 Å2
ΔGint-57.1 kcal/mol
Surface area95140 Å2
MethodPQS
Unit cell
Length a, b, c (Å)130.830, 130.830, 328.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsENZYME IS TRIMER IN SOLUTION

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Components

#1: Protein Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / Polynucleotide phosphorylase / PNPase


Mass: 81225.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BIFUNCTIONAL ENZYME POLYRIBONUCLEOTIDE NUCLEOTIDYL TRANSFERASE, ATP-GTP DIPHOSPHOTRANSFERASE
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Description: BIFUNCTIONAL ENZYME ISOLATED / Cellular location: CYTOPLASM / Gene: pnp, AFM16_28085 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: A0A1S9NJJ0, UniProt: Q53597*PLUS, polyribonucleotide nucleotidyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsARG A 31, SEQUENCING AMBIGUITY ILE A 156, SEQUENCING AMBIGUITY ILE A 210, SEQUENCING AMBIGUITY PHE ...ARG A 31, SEQUENCING AMBIGUITY ILE A 156, SEQUENCING AMBIGUITY ILE A 210, SEQUENCING AMBIGUITY PHE A 260, SEQUENCING AMBIGUITY LEU A 261, SEQUENCING AMBIGUITY ASP A 262, SEQUENCING AMBIGUITY TYR A 263, SEQUENCING AMBIGUITY GLN A 264, SEQUENCING AMBIGUITY ASP A 265, SEQUENCING AMBIGUITY VAL A 267, SEQUENCING AMBIGUITY LEU A 268, SEQUENCING AMBIGUITY GLU A 269, SEQUENCING AMBIGUITY ALA A 323, SEQUENCING AMBIGUITY LEU A 324, SEQUENCING AMBIGUITY THR A 325, SEQUENCING AMBIGUITY LYS A 326, SEQUENCING AMBIGUITY LEU A 328, SEQUENCING AMBIGUITY VAL A 329, SEQUENCING AMBIGUITY ARG A 330, SEQUENCING AMBIGUITY ALA A 335, SEQUENCING AMBIGUITY TYR A 409, SEQUENCING AMBIGUITY

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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: 3.33 Å3/Da / Density % sol: 54 %
Description: SELENOMETHIONINES WERE REPLACED WITH METHIONINES FOR MOLECULAR REPLACEMENT
Crystal growpH: 7
Details: 2.0M (NH4)2SO4, 100MM TRISHCL PH8.5, 100MM BISTRISHCL PH6.5, 60MM NACL, 4MM MGCL2, 5MM DTT, 50MM NA2W04, pH 7.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
215 mM1dropNaCl
32 Mammonium sulfate1reservoir
4100 mMTris-HCl1reservoir
55 mMdithiothreitol1reservoir
60.75 mM1reservoirNa2AsO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MSC / Wavelength: 1.5418
DetectorType: R-AXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 37642 / % possible obs: 99.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 59.1 Å2 / Rsym value: 0.079 / Net I/σ(I): 17.7
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.38 / % possible all: 92.3
Reflection
*PLUS
Num. measured all: 462572 / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3H

1e3h


Resolution: 2.5→19.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5669653.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT TARGET (MLF) INCLUDED ANOMALOUS DATA POOR DENSITY FOR RESIDUES 604 - 614 AND 623 - 634 WAS INTERPRETED FROM STRUCTURE OF HOMOLOGOUS DOMAIN PDB 1VIH. POOR DENSITY FOR RESIDUES 656 - ...Details: REFINEMENT TARGET (MLF) INCLUDED ANOMALOUS DATA POOR DENSITY FOR RESIDUES 604 - 614 AND 623 - 634 WAS INTERPRETED FROM STRUCTURE OF HOMOLOGOUS DOMAIN PDB 1VIH. POOR DENSITY FOR RESIDUES 656 - 661, 663 - 671, 675 - 679, AND 699 - 717 WAS INTERPRETED FROM STRUCTURE OF HOMOLOGOUS DOMAIN PDB 1SRO. MODEL HERE IS POLYALA (EXCEPT GLY AND PRO WHERE EXPECTED FROM SEQUENCE) WITH B-FACTOR SET TO 100.00 AND SUBJECT TO POSITIONAL REFINEMENT ONLY. AFTER POSITIONAL REFINEMENT RMSD CA ATOMS WERE 1.4 A (OVER 28 EQUIVALENT ATOMS) AND 1.6 (OVER 39 EQUIVALENT ATOMS) FOR 1VIH AND 1SRO HOMOLOGOUS DOMAINS RESPECTIVELY. THE C-TERMINAL RESIDUE WAS NOT SEEN IN ELECTRON DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1786 4.7 %RANDOM
Rwork0.213 ---
obs0.213 37642 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.0576 Å2 / ksol: 0.339268 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å24.69 Å20 Å2
2--3.62 Å20 Å2
3----7.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 55 305 5080
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 259 4.7 %
Rwork0.341 5201 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9A / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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