[English] 日本語
Yorodumi
- PDB-6zmj: Crystal structure of human GFAT-1 R203H -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zmj
TitleCrystal structure of human GFAT-1 R203H
ComponentsGlutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
KeywordsTRANSFERASE / Glutamine fructose-6-phosphate amidotransferase / GFAT / Ntn hydrolase
Function / homology
Function and homology information


Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / protein N-linked glycosylation ...Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / protein N-linked glycosylation / fructose 6-phosphate metabolic process / circadian regulation of gene expression / extracellular exosome / cytosol
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
GLUCOSE-6-PHOSPHATE / GLUTAMIC ACID / Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.774 Å
AuthorsRuegenberg, S. / Mayr, F. / Miethe, S. / Atanassov, I. / Baumann, U. / Denzel, M.S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research01GQ1423A Germany
European CommissionERC-2014-StG-640254-MetAGEn Germany
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
Citation
Journal: Nat Commun / Year: 2021
Title: Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1.
Authors: Ruegenberg, S. / Mayr, F.A.M.C. / Atanassov, I. / Baumann, U. / Denzel, M.S.
#1: Journal: Biorxiv / Year: 2020
Title: Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1
Authors: Ruegenberg, S. / Mayr, F. / Miethe, S. / Atanassov, I. / Baumann, U. / Denzel, M.S.
History
DepositionJul 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
B: Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,0215
Polymers155,3542
Non-polymers6673
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer, light scattering, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-22 kcal/mol
Surface area48690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.766, 152.766, 164.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 / D-fructose-6-phosphate amidotransferase 1 / Glutamine:fructose-6-phosphate amidotransferase 1 / ...D-fructose-6-phosphate amidotransferase 1 / Glutamine:fructose-6-phosphate amidotransferase 1 / GFAT1 / Hexosephosphate aminotransferase 1


Mass: 77676.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFPT1, GFAT, GFPT / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q06210, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Chemical ChemComp-G6Q / GLUCOSE-6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis tris propane pH 8.75, 0.2 M Potassium sodium tartrae, 20 % PEG3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.774→48.653 Å / Num. obs: 49792 / % possible obs: 99.75 % / Redundancy: 13.3 % / CC1/2: 0.997 / Net I/σ(I): 14.05
Reflection shellResolution: 2.774→2.873 Å / Num. unique obs: 4773 / CC1/2: 0.45

-
Processing

Software
NameVersionClassification
PHENIXdev_2499refinement
PDB_EXTRACT3.25data extraction
XDSMar 15, 2019data reduction
XDSMar 15, 2019data scaling
PHENIXdev_2499phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R4E

6r4e


Resolution: 2.774→48.653 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 1993 4 %
Rwork0.2005 47794 -
obs0.2021 49787 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 419.52 Å2 / Biso mean: 104.9774 Å2 / Biso min: 29.96 Å2
Refinement stepCycle: final / Resolution: 2.774→48.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10267 0 76 20 10363
Biso mean--64.68 42.46 -
Num. residues----1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210485
X-RAY DIFFRACTIONf_angle_d0.4514153
X-RAY DIFFRACTIONf_chiral_restr0.0421619
X-RAY DIFFRACTIONf_plane_restr0.0021817
X-RAY DIFFRACTIONf_dihedral_angle_d12.586366
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.774-2.84340.3641460.3292325297
2.8434-2.92030.32681200.3043371100
2.9203-3.00620.33241560.28033355100
3.0062-3.10320.31841530.2673366100
3.1032-3.21410.32651230.26543395100
3.2141-3.34270.31611440.24463377100
3.3427-3.49480.23981380.21783386100
3.4948-3.6790.24441390.19253402100
3.679-3.90940.20631490.17913403100
3.9094-4.21110.23111400.16473403100
4.2111-4.63460.20711380.15623452100
4.6346-5.30450.18631480.15293454100
5.3045-6.68040.24311470.20553501100
6.6804-48.6530.20691520.19463677100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3887-0.2986-0.02872.93290.04322.50710.09920.1992-0.1352-0.2572-0.1074-0.62450.22060.627-0.00860.39430.09930.09830.58560.08270.49885.440753.3538-74.1897
21.98250.710.27562.44590.13851.0087-0.02470.10530.29520.15340.04280.2555-0.1030.0104-0.00630.38270.0254-0.02510.34530.03570.3672-12.834751.3683-38.197
30.4215-0.39550.04340.6003-0.58351.2676-0.0047-0.9246-0.26210.946-0.07330.3216-0.0969-0.40860.05361.8837-0.15770.03511.90220.061.4065-12.542834.73779.8155
42.48740.50130.35391.84310.22791.2770.1452-0.0985-0.36680.4567-0.034-0.25660.13260.2074-0.10040.48180.0215-0.12740.34140.03590.42722.90329.7486-25.991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 314 )A2 - 314
2X-RAY DIFFRACTION2chain 'A' and (resid 315 through 672 )A315 - 672
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 314 )B2 - 314
4X-RAY DIFFRACTION4chain 'B' and (resid 315 through 680 )B315 - 680

+
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