[English] 日本語
Yorodumi
- PDB-8jjx: Crystal structure of QS-hNTAQ1 C28S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jjx
TitleCrystal structure of QS-hNTAQ1 C28S
ComponentsProtein N-terminal glutamine amidohydrolase
KeywordsHYDROLASE
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKang, J.M. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019R1A2C109025 Korea, Republic Of
CitationJournal: Protein Sci. / Year: 2024
Title: Structural study for substrate recognition of human N-terminal glutamine amidohydrolase 1 in the arginine N-degron pathway.
Authors: Kang, J.M. / Park, J.S. / Lee, J.S. / Jang, J.Y. / Han, B.W.
History
DepositionMay 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Protein N-terminal glutamine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)23,4311
Polymers23,4311
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.531, 64.539, 44.875
Angle α, β, γ (deg.)90.000, 98.220, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Protein N-terminal glutamine amidohydrolase


Mass: 23431.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gln-2 and Ser-1 are added to the N-terminus. / Source: (gene. exp.) Homo sapiens (human) / Gene: C8orf32 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024R9I8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, and 25 % (w/v) Polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 24745 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 22.07 Å2 / CC1/2: 0.99 / Net I/σ(I): 18.22
Reflection shellResolution: 1.7→1.77 Å / Num. unique obs: 2309 / CC1/2: 0.853

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40.11 Å / SU ML: 0.2067 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.0518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1938 1233 5 %
Rwork0.1681 23451 -
obs0.1694 24684 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.87 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 0 205 1838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711706
X-RAY DIFFRACTIONf_angle_d0.91972326
X-RAY DIFFRACTIONf_chiral_restr0.0664236
X-RAY DIFFRACTIONf_plane_restr0.0073305
X-RAY DIFFRACTIONf_dihedral_angle_d17.8523227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.31521230.28972334X-RAY DIFFRACTION88.83
1.77-1.850.26421400.23312631X-RAY DIFFRACTION98.89
1.85-1.950.26191360.19212614X-RAY DIFFRACTION99.53
1.95-2.070.21541370.18382622X-RAY DIFFRACTION99.6
2.07-2.230.25491380.18382631X-RAY DIFFRACTION99.75
2.23-2.460.18751380.17532632X-RAY DIFFRACTION99.68
2.46-2.810.20151390.17322652X-RAY DIFFRACTION99.89
2.81-3.540.17921390.15292632X-RAY DIFFRACTION99.82
3.54-40.110.15171430.14362703X-RAY DIFFRACTION99.68

+
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