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- PDB-3cdj: Crystal structure of the E. coli KH/S1 domain truncated PNPase -

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Basic information

Entry
Database: PDB / ID: 3cdj
TitleCrystal structure of the E. coli KH/S1 domain truncated PNPase
ComponentsPolynucleotide phosphorylase
KeywordsTRANSFERASE / Polynucleotide phosphorylase / mRNA turnover / RNase / RNA degradation / RNase PH domain / exoribonuclease / Kinase
Function / homology
Function and homology information


polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / bacterial degradosome / cyclic-di-GMP binding / RNA catabolic process / mRNA catabolic process / RNA processing / 3'-5'-RNA exonuclease activity / response to heat / magnesium ion binding ...polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / bacterial degradosome / cyclic-di-GMP binding / RNA catabolic process / mRNA catabolic process / RNA processing / 3'-5'-RNA exonuclease activity / response to heat / magnesium ion binding / RNA binding / membrane / identical protein binding / cytosol
Similarity search - Function
Helix Hairpins - #1490 / 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 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily ...Helix Hairpins - #1490 / 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 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 / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Helix Hairpins / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Helix non-globular / Special / K Homology domain / K homology RNA-binding domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShi, Z. / Yang, W.Z. / Lin-Chao, S. / Chak, K.F. / Yuan, H.S.
CitationJournal: Rna / Year: 2008
Title: Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation.
Authors: Shi, Z. / Yang, W.Z. / Lin-Chao, S. / Chak, K.F. / Yuan, H.S.
History
DepositionFeb 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polynucleotide phosphorylase


Theoretical massNumber of molelcules
Total (without water)61,0121
Polymers61,0121
Non-polymers00
Water64936
1
A: Polynucleotide phosphorylase

A: Polynucleotide phosphorylase

A: Polynucleotide phosphorylase


Theoretical massNumber of molelcules
Total (without water)183,0373
Polymers183,0373
Non-polymers00
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 area7610 Å2
ΔGint-37.2 kcal/mol
Surface area55580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.085, 160.085, 153.151
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Polynucleotide phosphorylase /


Mass: 61012.363 Da / Num. of mol.: 1 / Fragment: C terminal S1/KH truncated PNPase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pnp / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P05055*PLUS, polyribonucleotide nucleotidyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN THE UNIPROT.

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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: 3.09 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5M ammonium sulfate and 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 7, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 17783 / Num. obs: 17295 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.8→2.93 Å / Rmerge(I) obs: 0.34 / % possible all: 73

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3P

1e3p


Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1254 -RANDOM
Rwork0.27 ---
obs0.294 17295 92.3 %-
all-18740 --
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 0 36 3418
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_d2.873
X-RAY DIFFRACTIONc_mcbond_it2.285
X-RAY DIFFRACTIONc_mcangle_it4.127

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