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- PDB-1e3h: SeMet derivative of Streptomyces antibioticus PNPase/GPSI enzyme -

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Basic information

Entry
Database: PDB / ID: 1e3h
TitleSeMet derivative of Streptomyces antibioticus PNPase/GPSI enzyme
ComponentsGUANOSINE PENTAPHOSPHATE SYNTHETASE
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 / 3'-5'-RNA exonuclease activity / magnesium ion binding / RNA binding / cytosol
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 / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / 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
Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 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 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GUANOSINE PENTAPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,02810
Polymers82,1631
Non-polymers8659
Water5,242291
1
A: GUANOSINE PENTAPHOSPHATE SYNTHETASE
hetero molecules

A: GUANOSINE PENTAPHOSPHATE SYNTHETASE
hetero molecules

A: GUANOSINE PENTAPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,08430
Polymers246,4903
Non-polymers2,59427
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.610, 133.610, 344.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsBIOMOLECULEENZYME IS TRIMER IN SOLUTION

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Components

#1: Protein GUANOSINE PENTAPHOSPHATE SYNTHETASE / POLYNUCLEOTIDE PHOSPHORYLASE / GUANOSINE PENTAPHOSPHATE SYNTHETASE


Mass: 82163.297 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) / Strain: IMRU3720 / Description: BIFUNCTIONAL ENZYME ISOLATED / Cellular location: CYTOPLASM / Gene: GPSI / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q53597, polyribonucleotide nucleotidyltransferase, GTP diphosphokinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS IS A BIFUNCTIONAL ENZYME EC:2.7.7.8- POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE EC:2.7.6.5- ATP: ...THIS IS A BIFUNCTIONAL ENZYME EC:2.7.7.8- POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE EC:2.7.6.5- ATP:GTP 3'-PYROPHOSPHOTRANSFERASE
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: 3.6 Å3/Da / Density % sol: 60 %
Description: DATA STATISTICS ARE FOR LOW ENERGY REMOTE DATASET. INITIAL SE SUBSTRUCTURE MODEL FROM SHELX-90 SEARCH OF REVISE PATTERSON MAP.
Crystal growpH: 7
Details: 1.8M (NH4)2SO4, 100MM TRISHCL PH8.5, 100MM BISTRISHCL PH6.5, 60MM NACL, 4MM MGCL2, 5MM DTT., 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9740, 0.9791, 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9741
20.97911
30.981
ReflectionResolution: 2.6→38.99 Å / Num. obs: 36704 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 53.6 Å2 / Rsym value: 0.086 / Net I/σ(I): 5.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.59 / % possible all: 98.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNS0.9phasing
SHARPphasing
CNS0.9refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→38.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 9971455.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT TARGET (MLHL) INCLUDED WEIGHTED EXPERIMENTAL PHASE DISTRIBUTION ESTIMATES FROM SHARP POOR DENSITY FOR RESIDUES 605 - 614 AND 623 - 632 WAS INTERPRETED FROM MODEL OF HOMOLOGOUS ...Details: REFINEMENT TARGET (MLHL) INCLUDED WEIGHTED EXPERIMENTAL PHASE DISTRIBUTION ESTIMATES FROM SHARP POOR DENSITY FOR RESIDUES 605 - 614 AND 623 - 632 WAS INTERPRETED FROM MODEL OF HOMOLOGOUS DOMAIN PDB 1VIH POSITIONED BY HAND IN DENSITY. 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. THE C- TERMINAL RESIDUE WAS NOT SEEN IN DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1790 4.9 %RANDOM
Rwork0.201 ---
obs0.201 36704 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2064 Å2 / ksol: 0.327815 e/Å3
Displacement parametersBiso mean: 49.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å24.14 Å20 Å2
2---0.14 Å20 Å2
3---0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4502 0 45 291 4838
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.781.5
X-RAY DIFFRACTIONc_mcangle_it2.982
X-RAY DIFFRACTIONc_scbond_it3.12
X-RAY DIFFRACTIONc_scangle_it4.532.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 274 4.6 %
Rwork0.302 5691 -
obs--98.8 %
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: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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