[English] 日本語
Yorodumi
- PDB-9dsb: Crystal Structure of Spermin/spermidine N-Acetyltransferase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dsb
TitleCrystal Structure of Spermin/spermidine N-Acetyltransferase from Enterococcus faecalis V583
ComponentsSpermine/spermidine acetyltransferase
KeywordsTRANSFERASE / GCN5-related N-acetyltransferase (GNAT) / polyamine acetyltransferase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologySpermine/spermidine acetyltransferase, N-terminal / acyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETATE ION / : / Spermine/spermidine acetyltransferase, putative
Function and homology information
Biological speciesEnterococcus faecalis V583 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Kuhn, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of Spermin/spermidine N-Acetyltransferase from Enterococcus faecalis V583
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Kuhn, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionSep 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spermine/spermidine acetyltransferase
B: Spermine/spermidine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,92918
Polymers35,3722
Non-polymers55716
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.296, 90.296, 34.775
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Spermine/spermidine acetyltransferase


Mass: 17685.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis V583 (bacteria) / Strain: V583 / Gene: EF_1086 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL32 DE3 / Variant (production host): gold / References: UniProt: Q836M4

-
Non-polymers , 5 types, 178 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate pH 4.5, 3 M sodium Chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 47864 / % possible obs: 94.6 % / Redundancy: 9.7 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.016 / Rrim(I) all: 0.052 / Χ2: 0.507 / Net I/σ(I): 5.9 / Num. measured all: 466493
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.538.20.67317580.8850.9690.240.7160.46270
1.53-1.558.20.64218820.9130.9770.2290.6830.47474.2
1.55-1.587.80.61720130.9030.9740.2250.6580.47178.1
1.58-1.628.60.48221140.9520.9880.1660.5110.49485.7
1.62-1.658.70.45823580.9590.990.1580.4850.48991.9
1.65-1.699.10.40723750.9620.990.1390.4310.47996
1.69-1.739.20.34925810.9780.9940.1190.370.49898.9
1.73-1.789.70.31824870.9840.9960.1070.3360.49499.8
1.78-1.839.70.25925430.9890.9970.0870.2730.49999.7
1.83-1.899.10.20724960.9920.9980.0720.2190.51499.8
1.89-1.9610.60.16625470.9960.9990.0530.1740.49799.9
1.96-2.0410.60.12325320.9970.9990.040.130.599.9
2.04-2.1310.50.09124890.99810.0290.0960.49599.6
2.13-2.2410.40.07125560.99910.0230.0750.47899.8
2.24-2.389.70.05825080.99910.0190.0610.46999.6
2.38-2.5610.60.04725120.99910.0150.0490.45599.8
2.56-2.8210.90.04125500.99910.0130.0430.463100
2.82-3.2310.60.0332527110.0110.0350.46799.7
3.23-4.0710.20.03225180.99910.010.0330.58799.2
4.07-5010.80.03525180.99910.0110.0370.78299.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PHENIX1.21.2-5419refinement
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→39.1 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.506 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20358 2447 5.1 %RANDOM
Rwork0.16288 ---
obs0.16501 45414 94.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.637 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.5→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 19 162 2600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0122589
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162377
X-RAY DIFFRACTIONr_angle_refined_deg0.9641.8233496
X-RAY DIFFRACTIONr_angle_other_deg0.3731.7755446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.963518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62610466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0490.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02689
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5973.1571229
X-RAY DIFFRACTIONr_mcbond_other3.5953.1571227
X-RAY DIFFRACTIONr_mcangle_it5.8665.6651549
X-RAY DIFFRACTIONr_mcangle_other5.8645.6651550
X-RAY DIFFRACTIONr_scbond_it3.1083.3741360
X-RAY DIFFRACTIONr_scbond_other3.1073.3741361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0956.1551948
X-RAY DIFFRACTIONr_long_range_B_refined10.58733.133077
X-RAY DIFFRACTIONr_long_range_B_other10.27632.823047
X-RAY DIFFRACTIONr_rigid_bond_restr1.28934966
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 180 -
Rwork0.236 2442 -
obs--70.03 %

+
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