[English] 日本語
Yorodumi
- PDB-6vco: Crystal structure of E.coli RppH in complex with ppcpA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vco
TitleCrystal structure of E.coli RppH in complex with ppcpA
ComponentsRNA pyrophosphohydrolase
KeywordsRNA BINDING PROTEIN / RNA degradation
Function / homology
Function and homology information


RNA NAD-cap (NMN-forming) hydrolase activity / RNA destabilization / mRNA 5'-diphosphatase activity / RNA decapping / NAD-cap decapping / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / tRNA processing / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding / cytoplasm
Similarity search - Function
RNA pyrophosphohydrolase RppH / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...RNA pyrophosphohydrolase RppH / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM112940 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Authors: Gao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A.
History
DepositionDec 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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: RNA pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4712
Polymers18,9661
Non-polymers5051
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.140, 38.955, 57.734
Angle α, β, γ (deg.)90.000, 100.064, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein RNA pyrophosphohydrolase / (Di)nucleoside polyphosphate hydrolase / Ap5A pyrophosphatase


Mass: 18965.773 Da / Num. of mol.: 1 / Mutation: Q159A, E160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A776, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M (NH4)2SO4, 6.25% (v/v) PEG3350, and 5% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→19.48 Å / Num. obs: 18406 / % possible obs: 95.3 % / Redundancy: 7.1 % / Biso Wilson estimate: 22.06 Å2 / CC1/2: 0.999 / Net I/σ(I): 24
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 1706 / CC1/2: 0.923

-
Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2Y

4s2y


Resolution: 1.7→19.48 Å / SU ML: 0.1848 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.7444
RfactorNum. reflection% reflection
Rfree0.203 921 5 %
Rwork0.1717 --
obs0.1732 18402 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.57 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 31 153 1495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151379
X-RAY DIFFRACTIONf_angle_d1.19251871
X-RAY DIFFRACTIONf_chiral_restr0.065188
X-RAY DIFFRACTIONf_plane_restr0.0087233
X-RAY DIFFRACTIONf_dihedral_angle_d19.3389502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.790.24581220.21762316X-RAY DIFFRACTION90.36
1.79-1.90.27031280.20092432X-RAY DIFFRACTION93.29
1.9-2.050.22011300.18632461X-RAY DIFFRACTION94.53
2.05-2.250.20961300.17132479X-RAY DIFFRACTION95.36
2.25-2.580.20511340.16732548X-RAY DIFFRACTION96.65
2.58-3.250.21541350.17232559X-RAY DIFFRACTION97.89
3.25-19.480.181420.16182686X-RAY DIFFRACTION99.47

+
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