[English] 日本語
Yorodumi
- PDB-6qur: Mapping the allosteric communication network of aminodeoxychorism... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qur
TitleMapping the allosteric communication network of aminodeoxychorismate synthase
ComponentsGlutaminase
KeywordsTRANSFERASE / allostery / ancestral sequence reconstruction / catalytic triad / glutamine amidotransferases
Function / homologyClass I glutamine amidotransferase (GATase) domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsSemmelmann, F. / Straub, K. / Rajendran, C. / Nazet, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Mapping the Allosteric Communication Network of Aminodeoxychorismate Synthase.
Authors: Semmelmann, F. / Straub, K. / Nazet, J. / Rajendran, C. / Merkl, R. / Sterner, R.
History
DepositionFeb 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 25, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaminase


Theoretical massNumber of molelcules
Total (without water)22,3211
Polymers22,3211
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.755, 58.390, 71.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glutaminase


Mass: 22321.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.792→39.73 Å / Num. obs: 19372 / % possible obs: 99.87 % / Redundancy: 13 % / Biso Wilson estimate: 33.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06472 / Rpim(I) all: 0.01866 / Rrim(I) all: 0.06743 / Net I/σ(I): 23.52
Reflection shellResolution: 1.79→1.856 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.935 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 1880 / CC1/2: 0.866 / Rpim(I) all: 0.5803 / Rrim(I) all: 2.023 / % possible all: 99.16

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.792→39.73 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.89
RfactorNum. reflection% reflection
Rfree0.2671 969 5 %
Rwork0.2147 --
obs0.2173 19366 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.792→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 0 113 1632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071554
X-RAY DIFFRACTIONf_angle_d0.8862105
X-RAY DIFFRACTIONf_dihedral_angle_d3.084926
X-RAY DIFFRACTIONf_chiral_restr0.058237
X-RAY DIFFRACTIONf_plane_restr0.005271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7923-1.88680.35331360.31972579X-RAY DIFFRACTION99
1.8868-2.0050.32051350.26992567X-RAY DIFFRACTION100
2.005-2.15980.28841360.24112593X-RAY DIFFRACTION100
2.1598-2.37710.27191380.24622604X-RAY DIFFRACTION100
2.3771-2.72110.28031380.24362611X-RAY DIFFRACTION100
2.7211-3.42810.31631400.22392670X-RAY DIFFRACTION100
3.4281-45.26080.22371460.18072773X-RAY DIFFRACTION100

+
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://pdbjlvh1.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