[English] 日本語
Yorodumi
- PDB-9emt: Crystal structure of Histidine acetyltransferase with imidazole a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9emt
TitleCrystal structure of Histidine acetyltransferase with imidazole and coenzyme A disulfide
ComponentsProbable N-acetyltransferase 16
KeywordsTRANSFERASE / Acyltransferase / GNAT fold
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
: / Histidine N-acetyltransferase, C-terminal / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Chem-5NG / IMIDAZOLE / MALONATE ION / Probable N-acetyltransferase 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMyllykoski, M. / Arnesen, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)772039European Union
CitationJournal: To Be Published
Title: Human NAT16 encodes histidine alpha-acetyltransferase
Authors: Myllykoski, M. / Osberg, C. / Lundekvam, M. / Arnesen, T.
History
DepositionMar 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable N-acetyltransferase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0197
Polymers39,0381
Non-polymers1,9806
Water7,656425
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint6 kcal/mol
Surface area14930 Å2
Unit cell
Length a, b, c (Å)91.129, 91.129, 98.487
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Probable N-acetyltransferase 16


Mass: 39038.461 Da / Num. of mol.: 1 / Mutation: Residues 5-27 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAT16, C7orf52 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8N8M0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

-
Non-polymers , 5 types, 431 molecules

#2: Chemical ChemComp-5NG / [[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate / CoA-disulfide


Mass: 1533.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H70N14O32P6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Protein buffer: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% glycerol, 2 mM adenosine, 1 mM Ac-CoA. Well solution: 0.1 M MIB buffer pH 6.5, 20% PEG3350. Cryo-solution: 75% well solution, 25% glycerol
PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→41.8 Å / Num. obs: 90984 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 25.69 Å2 / CC1/2: 1 / Rrim(I) all: 0.048 / Net I/σ(I): 21.65
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 9 % / Mean I/σ(I) obs: 0.61 / Num. unique obs: 14572 / CC1/2: 0.326 / Rrim(I) all: 3.14 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSFeb 5, 2021data reduction
XDSFeb 5, 2021data scaling
PHASER2.8.3phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→41.78 Å / SU ML: 0.194 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1795 2275 2.5 %
Rwork0.1603 88687 -
obs0.1607 90962 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.9 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 126 425 3090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382864
X-RAY DIFFRACTIONf_angle_d0.83913918
X-RAY DIFFRACTIONf_chiral_restr0.0616418
X-RAY DIFFRACTIONf_plane_restr0.0179488
X-RAY DIFFRACTIONf_dihedral_angle_d16.5395489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.38371390.41765435X-RAY DIFFRACTION98.72
1.43-1.460.40771420.36565525X-RAY DIFFRACTION99.91
1.46-1.50.34061420.33125524X-RAY DIFFRACTION99.95
1.5-1.540.28131420.2645543X-RAY DIFFRACTION99.96
1.54-1.590.25271410.21885513X-RAY DIFFRACTION99.96
1.59-1.640.22391430.17815559X-RAY DIFFRACTION99.91
1.64-1.70.20591420.15745532X-RAY DIFFRACTION99.95
1.7-1.760.17261420.14475540X-RAY DIFFRACTION99.96
1.76-1.840.17961410.14475517X-RAY DIFFRACTION99.96
1.84-1.940.17471430.14725568X-RAY DIFFRACTION99.96
1.94-2.060.17051420.14175549X-RAY DIFFRACTION99.96
2.06-2.220.20471420.14125533X-RAY DIFFRACTION99.93
2.22-2.450.14621430.13945558X-RAY DIFFRACTION100
2.45-2.80.17981430.1455578X-RAY DIFFRACTION99.97
2.8-3.530.17091430.15585573X-RAY DIFFRACTION100
3.53-41.780.16531450.16135640X-RAY DIFFRACTION99.88

+
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