[English] 日本語
Yorodumi
- PDB-2ddz: Protein of Unknown Function from Pyrococcus horikoshi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ddz
TitleProtein of Unknown Function from Pyrococcus horikoshi
Components190aa long hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hexamer / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Protein of unknown function DUF366 / Domain of unknown function (DUF366) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANIDINE / : / DUF366 domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 Å
AuthorsRehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: X-ray structure of Unknown Protein from Pyrococcus horikoshi
Authors: Rehse, P.H. / Yokoyama, S.
History
DepositionFeb 7, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 190aa long hypothetical protein
B: 190aa long hypothetical protein
C: 190aa long hypothetical protein
D: 190aa long hypothetical protein
E: 190aa long hypothetical protein
F: 190aa long hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,07120
Polymers130,0466
Non-polymers1,02514
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23730 Å2
ΔGint-114 kcal/mol
Surface area40470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.756, 132.433, 135.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
190aa long hypothetical protein


Mass: 21674.264 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 (de3) / References: GenBank: 3256612, UniProt: O57962*PLUS
#2: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH5N3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12% PEG 4000, 100mM Tris-HCl, 100mM Guanidine HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B120.979121, 0.979443, 0.9830, 0.9770
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS1IMAGE PLATEJun 27, 2004mirrors
RIGAKU RAXIS2IMAGE PLATEJun 27, 2004mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111SINGLE WAVELENGTHMx-ray1
2Si111MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791211
30.9794431
40.9831
50.9771
ReflectionResolution: 2.24→50 Å / Num. all: 88916 / Num. obs: 88916 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.2
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 1.85 / Num. unique all: 8737 / % possible all: 99.2

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.24→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4175 4.7 %Ramdom
Rwork0.213 ---
all0.215 88916 --
obs0.215 82592 92.1 %-
Solvent computationBsol: 57.467 Å2
Displacement parametersBiso mean: 48.684 Å2
Baniso -1Baniso -2Baniso -3
1--19.898 Å20 Å20 Å2
2--16.344 Å20 Å2
3---3.554 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati sigma a obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.24→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9058 0 68 401 9527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0111
X-RAY DIFFRACTIONc_angle_deg1.44861
X-RAY DIFFRACTIONc_dihedral_angle_d23.92433
X-RAY DIFFRACTIONc_improper_angle_d0.86533
LS refinement shellResolution: 2.24→2.32 Å
RfactorNum. reflection% reflection
Rfree0.375 359 -
Rwork0.375 --
obs-6698 99.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4het.param

+
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