[English] 日本語
Yorodumi
- PDB-2pnz: Crystal structure of the P. abyssi exosome RNase PH ring complexe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pnz
TitleCrystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP
Components(Probable exosome complex exonuclease ...) x 2
Keywordshydrolase/hydrolase / RNase PH / hydrolase-hydrolase COMPLEX
Function / homology
Function and homology information


exosome (RNase complex) / RNA catabolic process / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / cytoplasm
Similarity search - Function
Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / 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 / Ribosomal Protein S5; domain 2 ...Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / 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 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Exosome complex component Rrp42 / Exosome complex component Rrp41
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsNavarro, M.V.A.S. / Guimaraes, B.G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Insights into the mechanism of progressive RNA degradation by the archaeal exosome.
Authors: Navarro, M.V.A.S. / Oliveira, C.C. / Zanchin, N.I. / Guimaraes, B.G.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3479
Polymers57,9892
Non-polymers1,3587
Water4,306239
1
A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules

A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules

A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,04227
Polymers173,9676
Non-polymers4,07521
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area23400 Å2
ΔGint-237.4 kcal/mol
Surface area57870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.810, 93.810, 126.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsThe biological assembly is a hexamer generated from the heterodimer in the asymmetric unit by the operations: -y, x-y+1, z and -x+y-1, -x, z

-
Components

-
Probable exosome complex exonuclease ... , 2 types, 2 molecules AB

#1: Protein Probable exosome complex exonuclease 1


Mass: 27720.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: Rrp41 / Plasmid: pET29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9V119, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein Probable exosome complex exonuclease 2


Mass: 30268.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: Rrp42 / Plasmid: pAE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9V118, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

-
Non-polymers , 4 types, 246 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris, 45% MPD and 0.1 M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.14→43.98 Å / Num. all: 36300 / Num. obs: 36060 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.8 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.172 / Net I/σ(I): 11.3
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 5542 / Rsym value: 0.639 / % possible all: 96

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BA0

2ba0


Resolution: 2.14→19.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.558 / SU ML: 0.157 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.205 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25481 1783 5 %RANDOM
Rwork0.18752 ---
all0.19088 34174 --
obs0.19088 33921 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.856 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.14→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 49 279 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224061
X-RAY DIFFRACTIONr_angle_refined_deg2.3122.0235507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8365511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.19624.848165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36915757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2321528
X-RAY DIFFRACTIONr_chiral_restr0.1640.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022940
X-RAY DIFFRACTIONr_nbd_refined0.2430.22348
X-RAY DIFFRACTIONr_nbtor_refined0.3230.22789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2323
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.224
X-RAY DIFFRACTIONr_mcbond_it1.0371.52593
X-RAY DIFFRACTIONr_mcangle_it1.59324087
X-RAY DIFFRACTIONr_scbond_it2.78731626
X-RAY DIFFRACTIONr_scangle_it4.0744.51415
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 115 -
Rwork0.244 2290 -
obs-2405 92.82 %
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)
12.7310.3736-0.00111.78150.30091.4795-0.0020.0771-0.1777-0.03660.0344-0.09290.3460.1191-0.0324-0.06380.0860.0197-0.1409-0.01390.0009-30.05763.3672-37.7559
21.91230.09480.48141.73330.14492.75220.0174-0.1352-0.06690.1254-0.0330.00080.278-0.10170.0156-0.0957-0.07470.0204-0.1730.0128-0.1558-60.71872.8566-30.7068
31.6032-0.0042-0.14170.35150.01630.5715-0.0455-0.0457-0.0595-0.01480.0213-0.06150.2363-0.00120.02420.0095-0.0102-0.0023-0.15590.0070.0152-48.05552.6847-33.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 2449 - 244
2X-RAY DIFFRACTION2BB8 - 27411 - 277
3X-RAY DIFFRACTION3A - BJ - K283 - 4201 - 139

+
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