[English] 日本語
Yorodumi
- PDB-4aid: Crystal structure of C. crescentus PNPase bound to RNase E recogn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aid
TitleCrystal structure of C. crescentus PNPase bound to RNase E recognition peptide
Components
  • POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
  • RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX
Function / homology
Function and homology information


ribonuclease E / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing ...ribonuclease E / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / Ribonuclease E / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E/G family / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain ...Polyribonucleotide nucleotidyltransferase, RNA-binding domain / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / Ribonuclease E / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E/G family / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / 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 / 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
PHOSPHATE ION / Ribonuclease E / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHardwick, S.W. / Gubbey, T. / Hug, I. / Jenal, U. / Luisi, B.F.
CitationJournal: Open Biol. / Year: 2012
Title: Crystal Structure of Caulobacter Crescentus Polynucleotide Phosphorylase Reveals a Mechanism of RNA Substrate Channelling and RNA Degradosome Assembly.
Authors: Hardwick, S.W. / Gubbey, T. / Hug, I. / Jenal, U. / Luisi, B.F.
History
DepositionFeb 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Other
Revision 1.2Feb 5, 2014Group: Database references / Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
B: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
C: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
F: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
G: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
H: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1579
Polymers239,8726
Non-polymers2853
Water3,621201
1
A: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
F: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

A: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
F: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

A: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
F: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1579
Polymers239,8726
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area14140 Å2
ΔGint-84.4 kcal/mol
Surface area68950 Å2
MethodPISA
2
B: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
G: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

B: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
G: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

B: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
G: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1579
Polymers239,8726
Non-polymers2853
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area14310 Å2
ΔGint-71.3 kcal/mol
Surface area66640 Å2
MethodPISA
3
C: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
H: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

C: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
H: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

C: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
H: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1579
Polymers239,8726
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area13070 Å2
ΔGint-86.5 kcal/mol
Surface area61410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.439, 157.439, 302.379
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE / PNPASE / POLYNUCLEOTIDE PHOSPHORYLASE


Mass: 78159.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER VIBRIOIDES (bacteria) / Strain: CB15 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9AC32, polyribonucleotide nucleotidyltransferase
#2: Protein/peptide RIBONUCLEASE, RNE/RNG FAMILY PROTEIN / RNASE E


Mass: 1798.081 Da / Num. of mol.: 3 / Fragment: PNPASE BINDING PEPTIDE - GWW, RESIDUES 885-898 / Source method: obtained synthetically / Source: (synth.) CAULOBACTER VIBRIOIDES (bacteria) / References: UniProt: Q9A749
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 19% WT/V PEG 3350, 0.15 M DL-MALIC ACID

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 85896 / % possible obs: 93.2 % / Observed criterion σ(I): 2.4 / Redundancy: 6.3 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 5.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GME

3gme


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.897 / SU B: 19.334 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.CHAIN C, RESIDUES 279-296 WERE DISORDERED AND WERE NOT MODELLED. NCS APPLIED AS AUTOMATICALLY GENERATED GLOBAL OPTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.25447 2322 3 %RANDOM
Rwork0.209 ---
obs0.21037 75066 89.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.002 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12436 0 15 201 12652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01912672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2651.97417189
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.93451684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27824.297491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.782152042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2891576
X-RAY DIFFRACTIONr_chiral_restr0.1440.21977
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219537
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 194 -
Rwork0.321 5615 -
obs--91.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.69470.271-0.06540.5326-0.08240.01590.0575-0.10570.0743-0.0091-0.05330.0713-0.01640.0299-0.00420.3302-0.00950.02080.3163-0.0010.1998-4.915725.2414-36.035
20.7061-0.28830.00670.5882-0.07140.01350.04440.0998-0.11810.0123-0.04190.09620.00540.0308-0.00260.33840.001-0.03830.30930.00410.1891-5.320665.4274-64.4244
32.0469-0.21380.10293.3556-0.69670.15830.00850.1899-0.1234-0.0751-0.00940.45560.01120.01680.00090.04470.02220.02270.1018-0.08350.777852.662646.5823-52.4007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 613
2X-RAY DIFFRACTION2B-1 - 556
3X-RAY DIFFRACTION3C-1 - 555

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more