[English] 日本語
Yorodumi
- PDB-1zs7: The structure of gene product APE0525 from Aeropyrum pernix -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zs7
TitleThe structure of gene product APE0525 from Aeropyrum pernix
Componentshypothetical protein APE0525Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Aeropyrum pernix / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


formation of translation preinitiation complex / translation initiation factor activity / RNA binding
Similarity search - Function
Domain of unknown function DUF1947 / Domain of unknown function (DUF1947) / Pre-PUA domain; domain 1 / Conserved hypothetical protein CHP03684 / Eukaryotic translation initiation factor 2D / MCT-1/Tma20 / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 ...Domain of unknown function DUF1947 / Domain of unknown function (DUF1947) / Pre-PUA domain; domain 1 / Conserved hypothetical protein CHP03684 / Eukaryotic translation initiation factor 2D / MCT-1/Tma20 / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / PUA-like superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / PUA domain-containing protein
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsCuff, M.E. / Skarina, T. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of gene product APE0525 from Aeropyrum pernix
Authors: Cuff, M.E. / Skarina, T. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionMay 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Apr 16, 2014Group: Data collection
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS NOT YET KNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein APE0525
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7617
Polymers21,2471
Non-polymers5146
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.850, 112.792, 39.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-401-

K

21A-435-

HOH

31A-451-

HOH

-
Components

#1: Protein hypothetical protein APE0525 / Hypothesis


Mass: 21247.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE0525 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YEQ6
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: K/Na Phosphate, glycerol, ethylene glycol, sucrose, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97940, 0.97959
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 14, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979591
ReflectionResolution: 1.85→36.9 Å / Num. all: 19171 / Num. obs: 19171 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.434 / % possible all: 79.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.85→36.86 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.652 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.123
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19883 933 5.2 %RANDOM
Rwork0.16668 ---
all0.1683 18045 --
obs0.1683 17112 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.906 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 26 246 1742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221570
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9882127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5535195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.9420.75866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87315281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4921521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021159
X-RAY DIFFRACTIONr_nbd_refined0.2090.2729
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21068
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2210
X-RAY DIFFRACTIONr_metal_ion_refined0.1810.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.222
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1810.22
X-RAY DIFFRACTIONr_mcbond_it0.6441.5953
X-RAY DIFFRACTIONr_mcangle_it1.2421528
X-RAY DIFFRACTIONr_scbond_it2.353623
X-RAY DIFFRACTIONr_scangle_it3.8654.5599
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 49 -
Rwork0.241 1113 -
obs--84.2 %
Refinement TLS params.Method: refined / Origin x: 47.697 Å / Origin y: 16.8719 Å / Origin z: -11.9229 Å
111213212223313233
T-0.0297 Å2-0.0116 Å2-0.0044 Å2--0.0274 Å2-0.0071 Å2---0.0392 Å2
L0.8714 °20.14 °2-0.496 °2-0.8416 °2-0.133 °2--0.6205 °2
S-0.0591 Å °0.0276 Å °-0.0374 Å °0.0186 Å °0.0341 Å °0.0334 Å °0.0266 Å °-0.0231 Å °0.025 Å °

+
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