[English] 日本語
Yorodumi
- PDB-1qmi: Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiqui... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qmi
TitleCrystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology
ComponentsRNA 3'-TERMINAL PHOSPHATE CYCLASE
KeywordsLIGASE / 2'3'CYCLIC PHOSPHATE RNA
Function / homology
Function and homology information


RNA 3'-terminal-phosphate cyclase (ATP) / RNA-3'-phosphate cyclase activity / RNA processing / ATP binding / cytoplasm
Similarity search - Function
RNA 3'-terminal phosphate cyclase type 1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain ...RNA 3'-terminal phosphate cyclase type 1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Dihydrodipicolinate Reductase; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA 3'-terminal phosphate cyclase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsPalm, G.J. / Billy, E. / Filipowicz, W. / Wlodawer, A.
CitationJournal: Structure / Year: 2000
Title: Crystal Structure of RNA 3'-Terminal Phosphate Cyclase, a Ubiquitous Enzyme with Unusual Topology
Authors: Palm, G.J. / Billy, E. / Filipowicz, W. / Wlodawer, A.
History
DepositionSep 28, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA 3'-TERMINAL PHOSPHATE CYCLASE
B: RNA 3'-TERMINAL PHOSPHATE CYCLASE
C: RNA 3'-TERMINAL PHOSPHATE CYCLASE
D: RNA 3'-TERMINAL PHOSPHATE CYCLASE


Theoretical massNumber of molelcules
Total (without water)148,9954
Polymers148,9954
Non-polymers00
Water00
1
A: RNA 3'-TERMINAL PHOSPHATE CYCLASE
B: RNA 3'-TERMINAL PHOSPHATE CYCLASE


Theoretical massNumber of molelcules
Total (without water)74,4972
Polymers74,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-7.7 kcal/mol
Surface area26670 Å2
MethodPISA
2
C: RNA 3'-TERMINAL PHOSPHATE CYCLASE
D: RNA 3'-TERMINAL PHOSPHATE CYCLASE


Theoretical massNumber of molelcules
Total (without water)74,4972
Polymers74,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-5.8 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.800, 126.600, 128.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.34768, -0.443579, -0.826049), (-0.595806, -0.575745, 0.55994), (-0.723971, 0.686845, -0.064112)195.6586, 70.0775, 116.6685
2given(0.999261, -0.034548, 0.016823), (0.034565, 0.999402, -0.000742), (-0.016787, 0.001323, 0.999858)49.3887, 0.1382, -5.1406
3given(-0.354289, -0.438311, -0.826052), (-0.572473, -0.596821, 0.562209), (-0.739428, 0.672078, -0.039474)182.37781, 37.849, 79.3294

-
Components

#1: Protein
RNA 3'-TERMINAL PHOSPHATE CYCLASE / RNA CYCLASE / RNA-3'-PHOSPHATE CYCLASE


Mass: 37248.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Cellular location: CYTOPLASM / Gene: RTCA / Plasmid: PET11D_ECOLI CYCLASE / Cellular location (production host): CYTOPLASM / Gene (production host): RTCA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P46849, RNA 3'-terminal-phosphate cyclase (ATP)
Has protein modificationY
Sequence detailsC-TERMINAL HIS TAG ADDED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 %
Crystal growpH: 5.5
Details: THE PROTEIN WAS CRYSTALLIZED FROM 13-15% MPEG2000, 200 MM NA-CITRATE PH 4.0, 200 MM TRIS/HCL PH 8.0, 2 MM DTT. PROTEIN CONCENTRATION WAS CA. 15 MG/ML.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
213-15 %mPEG20001reservoir
3200 mMNa citrate1reservoir
4200 mMTris-HCl1reservoir
52 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97942
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 41596 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 7.5 / % possible all: 91.6
Reflection
*PLUS
Num. measured all: 154068
Reflection shell
*PLUS
% possible obs: 91.6 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
X-PLOR3.1phasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2
Details: MODEL WAS NOT FULLY REFINED, THE HIS TAG IN CHAINS A,B,C,D WERE NOT VISIBLE IN THE ELECTRON DENSITY. THE CIS PEPTIDE GLY 232 - PRO 233 COULD ONLY BE MODELLED IN THE FULLY REFINED STRUCTURE 1QMH
RfactorNum. reflection% reflectionSelection details
Rfree0.331 1891 5 %RANDOM
Rwork0.244 ---
obs0.244 37201 89.8 %-
Displacement parametersBiso mean: 38.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9972 0 0 0 9972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS ONLY ON COORDINATES / Rms dev position: 0.48 Å / Weight position: 200
LS refinement shellResolution: 2.8→2.92 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.452 169 5 %
Rwork0.376 3342 -
obs--72 %

+
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