[English] 日本語
Yorodumi
- PDB-5xex: Crystal structure of S.aureus PNPase catalytic domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xex
TitleCrystal structure of S.aureus PNPase catalytic domain
ComponentsPolyribonucleotide nucleotidyltransferase
KeywordsTRANSFERASE / polynucleotide phosphorylase / catalytic domain
Function / homology
Function and homology information


polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / RNA catabolic process / mRNA catabolic process / RNA processing / 3'-5'-RNA exonuclease activity / magnesium ion binding / RNA binding / cytosol
Similarity search - Function
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 ...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 / RNA-binding domain, S1 / 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 / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PYROPHOSPHATE / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, X. / Zhang, X. / Zang, J.
CitationJournal: FEBS Lett. / Year: 2017
Title: Enolase binds to RnpA in competition with PNPase in Staphylococcus aureus
Authors: Wang, X. / Wang, C. / Wu, M. / Tian, T. / Cheng, T. / Zhang, X. / Zang, J.
History
DepositionApr 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Nov 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyribonucleotide nucleotidyltransferase
B: Polyribonucleotide nucleotidyltransferase
C: Polyribonucleotide nucleotidyltransferase
D: Polyribonucleotide nucleotidyltransferase
E: Polyribonucleotide nucleotidyltransferase
F: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,25524
Polymers372,9976
Non-polymers2,25718
Water4,360242
1
A: Polyribonucleotide nucleotidyltransferase
B: Polyribonucleotide nucleotidyltransferase
C: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,62712
Polymers186,4993
Non-polymers1,1299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-24 kcal/mol
Surface area62320 Å2
MethodPISA
2
D: Polyribonucleotide nucleotidyltransferase
E: Polyribonucleotide nucleotidyltransferase
F: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,62712
Polymers186,4993
Non-polymers1,1299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-24 kcal/mol
Surface area62840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.699, 93.773, 130.242
Angle α, β, γ (deg.)98.22, 95.34, 120.01
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 549
2010B3 - 549
1020A3 - 549
2020C3 - 549
1030A3 - 549
2030D3 - 549
1040A3 - 549
2040E3 - 549
1050A4 - 548
2050F4 - 548
1060B3 - 550
2060C3 - 550
1070B3 - 550
2070D3 - 550
1080B3 - 549
2080E3 - 549
1090B4 - 550
2090F4 - 550
10100C3 - 550
20100D3 - 550
10110C3 - 549
20110E3 - 549
10120C4 - 550
20120F4 - 550
10130D3 - 549
20130E3 - 549
10140D4 - 550
20140F4 - 550
10150E4 - 548
20150F4 - 548

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / PNPase


Mass: 62166.230 Da / Num. of mol.: 6 / Fragment: UNP residues 1-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: pnp, pnpA, SAOUHSC_01251 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: Q2FZ20, polyribonucleotide nucleotidyltransferase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H4O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M CaCl2, 0.1M HEPES, 28% (v/v) PEG 400, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97846 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97846 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 171703 / % possible obs: 91.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.5 / % possible all: 76.2

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CDI

3cdi


Resolution: 2.2→49.24 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.357 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24852 7966 5 %RANDOM
Rwork0.22287 ---
obs0.22416 150967 83.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.563 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å2-1.93 Å22.3 Å2
2---4.57 Å22.18 Å2
3---10.19 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23885 0 132 242 24259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01924453
X-RAY DIFFRACTIONr_bond_other_d00.0223768
X-RAY DIFFRACTIONr_angle_refined_deg1.471.98633017
X-RAY DIFFRACTIONr_angle_other_deg3.573354808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01853052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.31724.7881130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.011154436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2715180
X-RAY DIFFRACTIONr_chiral_restr0.0770.23756
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02127370
X-RAY DIFFRACTIONr_gen_planes_other0.0070.025102
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_it3.2515.0612280
X-RAY DIFFRACTIONr_mcbond_other3.2515.0612279
X-RAY DIFFRACTIONr_mcangle_it5.1237.57415308
X-RAY DIFFRACTIONr_mcangle_other5.1237.57415309
X-RAY DIFFRACTIONr_scbond_it3.6565.68612173
X-RAY DIFFRACTIONr_scbond_other3.6445.69112077
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9298.33517554
X-RAY DIFFRACTIONr_long_range_B_refined8.72240.87527109
X-RAY DIFFRACTIONr_long_range_B_other8.72240.87527109
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A336310.04
12B336310.04
21A336000.04
22C336000.04
31A334460.05
32D334460.05
41A334900.05
42E334900.05
51A334770.05
52F334770.05
61B336710.04
62C336710.04
71B335020.05
72D335020.05
81B334320.04
82E334320.04
91B335300.05
92F335300.05
101C335290.05
102D335290.05
111C334600.05
112E334600.05
121C335670.05
122F335670.05
131D334930.05
132E334930.05
141D334850.05
142F334850.05
151E334000.04
152F334000.04
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 428 -
Rwork0.284 7740 -
obs--58.33 %

+
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://pdbjlvh1.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