[English] 日本語
Yorodumi
- PDB-4nhl: Crystal structure of Tpa1p from Saccharomyces cerevisiae, termina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nhl
TitleCrystal structure of Tpa1p from Saccharomyces cerevisiae, termination and polyadenylation protein 1, in complex with N-oxalylglycine (NOG)
ComponentsPKHD-type hydroxylase TPA1
KeywordsOxidoreductase/Oxidoreductase inhibitor / 2-oxoglutarate oxygenase / oxygen sensing / protein synthesis regulation / double-stranded beta helix / jellyroll fold / prolyl hydroxylase / translation / ribosome / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


peptidyl-proline di-hydroxylation / peptidyl-proline dioxygenase activity / regulation of translational termination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / poly(A) binding / L-ascorbic acid binding / Protein hydroxylation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of translational fidelity / translational termination ...peptidyl-proline di-hydroxylation / peptidyl-proline dioxygenase activity / regulation of translational termination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / poly(A) binding / L-ascorbic acid binding / Protein hydroxylation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of translational fidelity / translational termination / ferrous iron binding / nucleus / cytoplasm
Similarity search - Function
Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / TPA1/Ofd1, C-terminal / Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / Double-stranded beta-helix / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain ...Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / TPA1/Ofd1, C-terminal / Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / Double-stranded beta-helix / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / 4-Layer Sandwich / Jelly Rolls / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Prolyl 3,4-dihydroxylase TPA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.84 Å
AuthorsScotti, J.S. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Structure / Year: 2015
Title: Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases.
Authors: Horita, S. / Scotti, J.S. / Thinnes, C. / Mottaghi-Taromsari, Y.S. / Thalhammer, A. / Ge, W. / Aik, W. / Loenarz, C. / Schofield, C.J. / McDonough, M.A.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: PKHD-type hydroxylase TPA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6973
Polymers74,4951
Non-polymers2022
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.216, 67.251, 70.976
Angle α, β, γ (deg.)90.000, 105.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-842-

HOH

-
Components

#1: Protein PKHD-type hydroxylase TPA1 / Termination and polyadenylation protein 1


Mass: 74494.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: TPA1, YER049W / Plasmid: pNIC28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P40032, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8 mM MnCl2, 1.1 mM OGA, 0.1 M succinic acid, 12% PEG 3350, vapor diffusion sitting drop, temperature 293K, pH 7.0, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.84→30 Å / Num. all: 18339 / Num. obs: 18332 / % possible obs: 99.96 % / Redundancy: 3.7 % / Biso Wilson estimate: 44.543 Å2 / Rmerge(I) obs: 0.178 / Χ2: 1.141 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.84-2.940.682.0618061.174100
2.94-3.060.532.7118261.263100
3.06-3.20.4393.1618091.161100
3.2-3.370.3134.4918401.169100
3.37-3.580.2256.1918121.204100
3.58-3.850.197.0818191.20899.9
3.85-4.240.1667.7418501.107100
4.24-4.850.1358.9318251.07299.7
4.85-6.10.1269.8718561.00799.9
6.1-300.07814.918891.054100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3KT7

3kt7


Resolution: 2.84→29.7 Å / Occupancy max: 1 / Occupancy min: 0.5
RfactorNum. reflectionSelection details
Rfree0.2425 1834 Random
Rwork0.181 --
obs-18325 -
Displacement parametersBiso max: 84.96 Å2 / Biso mean: 42.6496 Å2 / Biso min: 26.35 Å2
Refinement stepCycle: LAST / Resolution: 2.84→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 11 74 4453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.282
LS refinement shellResolution: 2.83→2.9 Å
RfactorNum. reflection% reflection
Rfree0.3478 125 -
Rwork0.2672 --
obs-1251 89 %

+
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