[English] 日本語
Yorodumi
- PDB-1i21: CRYSTAL STRUCTURE OF YEAST GNA1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i21
TitleCRYSTAL STRUCTURE OF YEAST GNA1
ComponentsGLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / ALPHA/BETA / DOMAIN SWAPPING / GNAT
Function / homology
Function and homology information


Synthesis of UDP-N-acetyl-glucosamine / glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process / nucleus / cytoplasm
Similarity search - Function
Glucosamine 6-phosphate N-acetyltransferase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucosamine 6-phosphate N-acetyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsPeneff, C. / Mengin-Lecreulx, D. / Bourne, Y.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The crystal structures of Apo and complexed Saccharomyces cerevisiae GNA1 shed light on the catalytic mechanism of an amino-sugar N-acetyltransferase.
Authors: Peneff, C. / Mengin-Lecreulx, D. / Bourne, Y.
History
DepositionFeb 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
B: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
M: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
N: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
X: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
Y: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)110,4396
Polymers110,4396
Non-polymers00
Water4,936274
1
A: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
B: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)36,8132
Polymers36,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-34 kcal/mol
Surface area14020 Å2
MethodPISA
2
M: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
N: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)36,8132
Polymers36,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-34 kcal/mol
Surface area13900 Å2
MethodPISA
3
X: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
Y: GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)36,8132
Polymers36,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-32 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.584, 93.648, 168.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE / PHOSPHOGLUCOSAMINE TRANSACETYLASE / PHOSPHOGLUCOSAMINE ACETYLASE


Mass: 18406.418 Da / Num. of mol.: 6 / Mutation: S39C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YFL017C / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (PREP 4)
References: UniProt: P43577, glucosamine-phosphate N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEG 600, IMIDAZOLE, MALATE, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117-22 %PEG6001reservoir
20.2 Mimidazole1reservoir
30.4 Mmalate1reservoir
410 mMTris-HCl1drop
5150 mM1dropNaCl
61 mMdithiothreitol1drop
710 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9324 / Wavelength: 0.9324 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9324 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 37568 / % possible obs: 92.6 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 26.7 Å2 / Rsym value: 5.7 / Net I/σ(I): 6.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 4.8 / Rsym value: 14.1 / % possible all: 91.5
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 91.6 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 4.8

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.86 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1733447.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1886 5 %RANDOM
Rwork0.212 ---
obs0.212 37830 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.17 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--6.74 Å20 Å20 Å2
2--13.61 Å20 Å2
3----6.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7358 0 0 274 7632
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.07
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 337 5.6 %
Rwork0.269 5733 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / Num. reflection Rfree: 1887 / % reflection Rfree: 5 % / Rfactor obs: 0.221 / Rfactor Rfree: 0.287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor Rfree: 0.365 / % reflection Rfree: 5.6 % / Rfactor Rwork: 0.269

+
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