[English] 日本語
Yorodumi
- PDB-2fc3: Crystal structure of the extremely thermostable Aeropyrum pernix ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fc3
TitleCrystal structure of the extremely thermostable Aeropyrum pernix L7Ae multifunctional protein
Components50S ribosomal protein L7Ae
KeywordsRIBOSOME / RNA BINDING PROTEIN / alpha-beta-alpha sandwich
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBrown II, B.A. / Suryadi, J. / Zhou, Z. / Gupton Jr., T.B. / Flowers, S.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the Aeropyrum pernix L7Ae multifunctional protein and insight into its extreme thermostability.
Authors: Bhuiya, M.W. / Suryadi, J. / Zhou, Z. / Brown, B.A.
History
DepositionDec 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 11, 2013Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 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: 50S ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)13,6281
Polymers13,6281
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.054, 49.188, 65.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 50S ribosomal protein L7Ae


Mass: 13627.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: rpl7ae / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q9YAX7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 10% Isopropanol, 100 mM HEPES-KOH, pH 7.5, 1 mM ZnCl2 mixed 1:2 with 500 microMolar L7Ae protein, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 6, 2004 / Details: Osmic Confocal Blue Max-Flux
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.54→65.05 Å / Num. all: 34157 / Num. obs: 13926 / % possible obs: 81.5 % / Observed criterion σ(I): 3 / Redundancy: 2.45 % / Biso Wilson estimate: 17.53 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 23.7
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 1.08 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1678 / % possible all: 15.8

-
Phasing

Phasing MRRfactor: 0.463 / Cor.coef. Fo:Fc: 0.535
Highest resolutionLowest resolution
Translation4 Å50 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
CrystalClearV. 1.3.6 (MSC/RIGAKU)data reduction
CrystalClearV. 1.3.6 (MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XBI

1xbi


Resolution: 1.56→32.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.913 / SU ML: 0.064 / Isotropic thermal model: ISOTROPIC OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R: 0.157 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 695 5.1 %RANDOM
Rwork0.174 ---
all0.177 13760 --
obs0.177 13737 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.807 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.56 Å20 Å2
3---0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.56→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 0 119 1076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022970
X-RAY DIFFRACTIONr_bond_other_d0.0010.02689
X-RAY DIFFRACTIONr_angle_refined_deg1.4192.0121311
X-RAY DIFFRACTIONr_angle_other_deg0.92831693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.43924.05437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01615185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.801158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02171
X-RAY DIFFRACTIONr_nbd_refined0.210.2208
X-RAY DIFFRACTIONr_nbd_other0.1930.2739
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2493
X-RAY DIFFRACTIONr_nbtor_other0.0820.2506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0490.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3630.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.29
X-RAY DIFFRACTIONr_mcbond_it1.5421.5808
X-RAY DIFFRACTIONr_mcbond_other0.4311.5249
X-RAY DIFFRACTIONr_mcangle_it1.82221007
X-RAY DIFFRACTIONr_scbond_it3.1613389
X-RAY DIFFRACTIONr_scangle_it4.6344.5304
X-RAY DIFFRACTIONr_rigid_bond_restr2.13231947
X-RAY DIFFRACTIONr_sphericity_free11.2865119
X-RAY DIFFRACTIONr_sphericity_bonded3.04251646
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.875 10 -
Rwork0.243 217 -
obs-227 93.42 %

+
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