[English] 日本語
Yorodumi
- PDB-6l7q: Crystal structure of a hypothetical protein PYCH_01220 derived fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l7q
TitleCrystal structure of a hypothetical protein PYCH_01220 derived from Pyrococcus yayanosii
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / cytosolic protein / hypothetical protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPyrococcus yayanosii
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.16 Å
AuthorsJeon, J.-H. / Noh, H. / Oh, B.-H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2018R1A2B3004764 Korea, Republic Of
CitationJournal: Proteins / Year: 2021
Title: Crystal structure of PYCH_01220 from Pyrococcus yayanosii potentially involved in binding nucleic acid.
Authors: Noh, H. / Jeon, J.H. / Kim, Y.G. / Oh, B.H.
History
DepositionNov 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 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: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)17,0121
Polymers17,0121
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.278, 86.278, 62.438
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein hypothetical protein /


Mass: 17012.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus yayanosii (strain CH1 / JCM 16557) (archaea)
Strain: CH1 / JCM 16557 / Gene: PYCH_01220 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8AFT0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris (pH 8.5), 0.05M Magnesium sulfate, 1.8M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.16→23.956 Å / Num. obs: 51395 / % possible obs: 85.65 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.06 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Χ2: 1.8 / Net I/σ(I): 24.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.16-1.183.10.26730000.7440.140.3041.10973.3
1.18-1.213.30.25630520.7920.1320.291.23375.8
1.21-1.243.90.29231480.7250.1380.3251.877.7
1.24-1.283.80.2232890.8680.1090.2471.27681.2
1.28-1.324.40.2333280.890.1040.2541.98382.3
1.32-1.3750.15535940.9640.0670.171.17789.2
1.37-1.435.40.12837310.9790.0540.1391.12991.5
1.43-1.4960.12437860.9840.050.1341.50994
1.49-1.575.90.09838920.9910.040.1061.64296.1
1.57-1.676.90.08739490.9940.0320.0931.84497.4
1.67-1.87.90.07639990.9960.0260.082.02499
1.8-1.987.20.06828580.9960.0250.0732.2970.6
1.98-2.268.10.0633260.9980.0210.0642.5681.8
2.26-2.859.50.05137900.9990.0170.0542.50194
2.85-509.30.04331880.9990.0150.0452.36178.7

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.10.1_2155phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.16→23.956 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.41 / Phase error: 17.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 1647 3.2 %
Rwork0.1916 49748 -
obs0.192 51395 85.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 39.64 Å2 / Biso mean: 16.4946 Å2 / Biso min: 7.71 Å2
Refinement stepCycle: final / Resolution: 1.16→23.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 0 184 1374
Biso mean---23.67 -
Num. residues----145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.16-1.19420.21011160.2197358774
1.1942-1.23270.2691260.239370076
1.2327-1.27670.21631290.1996388180
1.2767-1.32790.21961360.214402483
1.3279-1.38830.20061450.1833431989
1.3883-1.46150.19341540.1757451193
1.4615-1.5530.17781520.1743459795
1.553-1.67290.21071520.1711472397
1.6729-1.84120.20581560.1824479399
1.8412-2.10750.18561210.1861369176
2.1075-2.65470.21031280.1953390080
2.6547-23.9560.20591320.1971402283

+
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