[English] 日本語
Yorodumi
- PDB-4af1: Archeal Release Factor aRF1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4af1
TitleArcheal Release Factor aRF1
ComponentsPEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1
KeywordsHYDROLASE / TRANSLATION
Function / homology
Function and homology information


translation release factor complex / translation release factor activity, codon specific / sequence-specific mRNA binding / cytosol / cytoplasm
Similarity search - Function
Peptide chain release factor aRF1 / eRF1 domain 2 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 ...Peptide chain release factor aRF1 / eRF1 domain 2 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / 50S ribosomal protein L30e-like / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptide chain release factor subunit 1 / Peptide chain release factor subunit 1
Similarity search - Component
Biological speciesHALOBACTERIUM SALINARUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKarlsen, J.L. / Kjeldgaard, M.
CitationJournal: To be Published
Title: Archeal Release Factor Arf1 Contains a Metal Binding Domain
Authors: Karlsen, J.L. / Kjeldgaard, M.
History
DepositionJan 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7582
Polymers46,6921
Non-polymers651
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.020, 31.990, 111.150
Angle α, β, γ (deg.)90.00, 113.47, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 / TRANSLATION TERMINATION FACTOR ARF1 / RELEASE FACTOR 1


Mass: 46692.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HALOBACTERIUM SALINARUM (Halophile) / Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS RIL
References: UniProt: Q9HNF0, UniProt: B0R748*PLUS, protein-synthesizing GTPase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.8 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: VAPOR DIFFUSION IN SITTING DROPS WITH RESERVOIR CONTAINING 1.8-2.2 M NA MALONATE (PH 8), 50 MM MES PH 6.5, 7 MM 2-MERCAPTOETHANOL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2→64.16 Å / Num. obs: 29222 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 29.24 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2.3 / % possible all: 48

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
UCLAMBI DIFFRACTION ANISOTROPY SERVERdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT9

1dt9


Resolution: 2→64.16 Å / SU ML: 0.3 / σ(F): 2 / Phase error: 31.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2788 1385 5 %
Rwork0.2537 --
obs0.255 29073 94.7 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.468 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0427 Å20 Å2-0.2722 Å2
2--2.1956 Å20 Å2
3----2.2384 Å2
Refinement stepCycle: LAST / Resolution: 2→64.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 1 181 3405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043284
X-RAY DIFFRACTIONf_angle_d1.0884439
X-RAY DIFFRACTIONf_dihedral_angle_d13.5591236
X-RAY DIFFRACTIONf_chiral_restr0.055480
X-RAY DIFFRACTIONf_plane_restr0.003596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0026-2.07410.3981780.38161485X-RAY DIFFRACTION55
2.0741-2.15720.38251380.3532635X-RAY DIFFRACTION95
2.1572-2.25530.34351440.33162724X-RAY DIFFRACTION99
2.2553-2.37430.33371420.32282691X-RAY DIFFRACTION99
2.3743-2.5230.37771450.31342760X-RAY DIFFRACTION100
2.523-2.71780.38321450.31352748X-RAY DIFFRACTION100
2.7178-2.99130.32071450.29052757X-RAY DIFFRACTION100
2.9913-3.4240.24821460.23582790X-RAY DIFFRACTION100
3.424-4.31360.2421480.20352803X-RAY DIFFRACTION100
4.3136-51.02510.21351540.20282919X-RAY DIFFRACTION100
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)
10.10360.0508-0.07050.21920.08670.2715-0.30160.03340.0719-0.13450.26250.3388-0.21981.0557-0.04380.13740.02410.0150.2977-0.07830.073723.7272-3.71844.3788
20.06330.0391-0.00730.1810.04110.07730.40960.13870.29870.3076-0.26280.18740.12440.24070.00140.16030.07030.00440.681-0.01230.207150.926-7.036112.0916
30.3417-0.04170.0850.32410.19690.50420.5609-0.1440.01160.2855-0.3372-0.65730.6933-0.48040.17460.2478-0.0394-0.07190.0304-0.03750.12079.4273-21.314722.0064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 6:144
2X-RAY DIFFRACTION2CHAIN A AND RESID 145:279
3X-RAY DIFFRACTION3CHAIN A AND RESID 280:500

+
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