[English] 日本語
Yorodumi
- PDB-1ng6: Structure of Cytosolic Protein of Unknown Function YqeY from Baci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ng6
TitleStructure of Cytosolic Protein of Unknown Function YqeY from Bacillus subtilis
ComponentsHypothetical protein yqeY
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Domain GatB/Yqey / pfam02637 / DUF186 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


carbon-nitrogen ligase activity, with glutamine as amido-N-donor
Similarity search - Function
Uncharacterised protein YqeY/AIM41, N-terminal domain / Uncharacterised protein YqeY/Aim41 / YqeY/Aim41, N-terminal domain / Yqey-like protein / Arc Repressor Mutant, subunit A - #410 / Hypothetical Protein Yqey; Chain: A; domain1 / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein YqeY
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsZhang, R. / Dementiva, I. / Vinokour, E. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.4A crystal structure of hypothetical cytosolic protein YQEY
Authors: Zhang, R. / Dementiva, I. / Vinokour, E. / Collart, F. / Joachimiak, A.
History
DepositionDec 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 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 yqeY


Theoretical massNumber of molelcules
Total (without water)16,7911
Polymers16,7911
Non-polymers00
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.463, 45.820, 44.361
Angle α, β, γ (deg.)90.00, 101.85, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein (APC1524) existed as monomer. One molecule in asymmetric unit.

-
Components

#1: Protein Hypothetical protein yqeY


Mass: 16791.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YQEY / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P54464
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 19%PEG3350, 5% PEG400, 0.1M Bis Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Dec 15, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.946561
ReflectionResolution: 1.4→50 Å / Num. all: 27607 / Num. obs: 27414 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.95 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 30
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2661 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→34.71 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The number of reflections for refinement is greater than the number of reflections for data collection because in cns refinement (hlml target), the Fridel's pair was treated as two seperated reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2538 4.9 %RANDOM
Rwork0.21 ---
obs0.21 51310 95 %-
all-54010 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5572 Å2 / ksol: 0.336155 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å21.34 Å2
2--0.63 Å20 Å2
3---0.19 Å2
Refine analyzeLuzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.4→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 0 295 1464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d16.1
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.422.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 371 4.8 %
Rwork0.298 7336 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.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