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- PDB-1e3p: tungstate derivative of Streptomyces antibioticus PNPase/GPSI enzyme -
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Open data
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Basic information
Entry | Database: PDB / ID: 1e3p | ||||||
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Title | tungstate derivative of Streptomyces antibioticus PNPase/GPSI enzyme | ||||||
![]() | Polyribonucleotide nucleotidyltransferase | ||||||
![]() | POLYRIBONUCLEOTIDE TRANSFERASE / ATP-GTP DIPHOSPHOTRANSFERASE RNA PROCESSING / RNA DEGRADATION | ||||||
Function / homology | ![]() polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / mRNA catabolic process / RNA processing / 3'-5'-RNA exonuclease activity / magnesium ion binding / RNA binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Symmons, M.F. / Jones, G.H. / Luisi, B.F. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.1 KB | Display | ![]() |
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PDB format | ![]() | 108 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.9 KB | Display | ![]() |
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Full document | ![]() | 473.1 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e3hSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | ENZYME IS TRIMER IN SOLUTION |
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Components
#1: Protein | 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.) ![]() ![]() ![]() References: UniProt: A0A1S9NJJ0, UniProt: Q53597*PLUS, polyribonucleotide nucleotidyltransferase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-WO4 / | #4: Water | ChemComp-HOH / | Sequence details | ARG A 31, SEQUENCING AMBIGUITY ILE A 156, SEQUENCING AMBIGUITY ILE A 210, SEQUENCING AMBIGUITY PHE ...ARG A 31, SEQUENCING | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 54 % Description: SELENOMETHIONINES WERE REPLACED WITH METHIONINES FOR MOLECULAR REPLACEMENT | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: R-AXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: YALE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.0576 Å2 / ksol: 0.339268 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9A / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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