[English] 日本語
Yorodumi
- PDB-2p38: Crystal Structure of Pyrococcus Abyssi Protein Homologue of Sacch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p38
TitleCrystal Structure of Pyrococcus Abyssi Protein Homologue of Saccharomyces Cerevisiae NIP7P
ComponentsProtein involved in ribosomal biogenesis
KeywordsBIOSYNTHETIC PROTEIN / TWO ALPHA/BETA DOMAINS / PUA DOMAIN
Function / homology
Function and homology information


PaNip7 pre-PUA domain / Nuclear Transport Factor 2; Chain: A, - #220 / PUA domain / UPF0113 PUA domain / UPF0113, PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Roll ...PaNip7 pre-PUA domain / Nuclear Transport Factor 2; Chain: A, - #220 / PUA domain / UPF0113 PUA domain / UPF0113, PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein involved in ribosomal biogenesis
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsGuimaraes, B.G. / Coltri, P.P. / Oliveira, C.C. / Zanchin, N.I.T.
CitationJournal: Biochemistry / Year: 2007
Title: Structural Insights into the Interaction of the Nip7 PUA Domain with Polyuridine RNA
Authors: Coltri, P.P. / Guimaraes, B.G. / Granato, D.C. / Luz, J.S. / Teixeira, E.C. / Oliveira, C.C. / Zanchin, N.I.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein involved in ribosomal biogenesis
B: Protein involved in ribosomal biogenesis


Theoretical massNumber of molelcules
Total (without water)38,6392
Polymers38,6392
Non-polymers00
Water4,468248
1
A: Protein involved in ribosomal biogenesis
B: Protein involved in ribosomal biogenesis

A: Protein involved in ribosomal biogenesis
B: Protein involved in ribosomal biogenesis


Theoretical massNumber of molelcules
Total (without water)77,2784
Polymers77,2784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)88.492, 90.284, 63.347
Angle α, β, γ (deg.)90.00, 134.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-276-

HOH

21B-177-

HOH

31B-215-

HOH

-
Components

#1: Protein Protein involved in ribosomal biogenesis


Mass: 19319.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Plasmid: PCYTEXP3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q9V219
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growpH: 7.2
Details: 4.1 M NACL, 100 MM HEPES, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 7.20

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2004
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.8→31.67 Å / Num. obs: 33002 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.049
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7 % / Rsym value: 0.301 / % possible all: 100

-
Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.1.24refinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→31.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.903 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1673 5.1 %RANDOM
Rwork0.207 ---
obs0.21 31334 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 0 248 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222495
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9553386
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021883
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.21420
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1171.51538
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98222467
X-RAY DIFFRACTIONr_scbond_it3.0833957
X-RAY DIFFRACTIONr_scangle_it5.0984.5919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 118
Rwork0.309 2330

+
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