[English] 日本語
Yorodumi
- PDB-4jjx: Dodecameric structure of spermidine N-acetyltransferase SpeG from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jjx
TitleDodecameric structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae O1 biovar eltor
ComponentsSpermidine n1-acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


spermidine catabolic process / spermine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / polyamine catabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Kuhn, M.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Mol.Biol. / Year: 2015
Title: A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure.
Authors: Filippova, E.V. / Kuhn, M.L. / Osipiuk, J. / Kiryukhina, O. / Joachimiak, A. / Ballicora, M.A. / Anderson, W.F.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)62,9273
Polymers62,9273
Non-polymers00
Water46826
1
A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)251,70812
Polymers251,70812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area31500 Å2
ΔGint-80 kcal/mol
Surface area84300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.524, 131.524, 72.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Spermidine n1-acetyltransferase


Mass: 20975.646 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9KL03
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 45% Ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2012 / Details: Beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.82→30 Å / Num. all: 15565 / Num. obs: 15565 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 68.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.4
Reflection shellResolution: 2.82→2.87 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / Num. unique all: 1469 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EG7

3eg7
PDB Unreleased entry


Resolution: 2.83→29.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 36.217 / SU ML: 0.321 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26479 774 5 %RANDOM
Rwork0.19372 ---
obs0.19729 14686 98.21 %-
all-14686 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å2-0 Å2
2---1.64 Å20 Å2
3---3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.83→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 0 26 4314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194398
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9345938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98923.977264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32315771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9361535
X-RAY DIFFRACTIONr_chiral_restr0.0960.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023439
LS refinement shellResolution: 2.83→2.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 54 -
Rwork0.303 1048 -
obs--96.58 %
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)
13.5466-0.14332.205210.04882.06633.78140.02670.3549-0.292-0.1404-0.1540.6296-0.206-0.1370.12730.1233-0.0050.05670.1494-0.10280.2623-17.0793-21.617313.1656
23.75791.68821.168911.9817-2.52074.74940.5883-0.46040.81780.9233-0.38911.1032-0.9697-0.0043-0.19920.4165-0.05550.22420.1987-0.14230.2942-17.5816-12.761224.6033
31.77381.2322-2.81834.945-3.227510.62180.26860.10250.2088-0.0884-0.30980.0647-0.46830.31640.04120.07070.03360.0140.1165-0.06440.2831-18.3107-28.096518.9647
42.5584-2.0672-2.14852.32040.74453.41950.1310.2335-0.3361-0.2064-0.25120.4281-0.0298-0.01490.12010.1193-0.057-0.08890.1137-0.03560.2116-26.9803-32.860727.2077
55.706-0.07491.65753.0302-0.53793.54030.07080.14650.08280.035-0.02490.390.4162-0.3889-0.04590.143-0.0834-0.01750.07860.01240.06925.4406-22.592221.2337
64.7317-0.31482.96462.6896-2.638212.6526-0.06880.3108-0.3309-0.4689-0.0607-0.1211-0.2307-0.29910.12950.1350.03220.0270.069-0.0530.063613.8261-29.147319.885
74.81049.54520.309521.3558-8.409433.7762-0.5849-0.0860.2436-1.3638-0.42320.2190.74270.76191.00810.42260.25350.06710.3926-0.13060.233614.6595-38.956810.0602
83.52212.1725-0.59222.8904-0.2712.92880.06730.4485-0.4419-0.14160.0017-0.34960.17530.3546-0.0690.04670.074-0.01890.1783-0.06110.088814.1374-40.193326.7441
98.84788.73373.41149.20496.283515.8949-0.3260.3161-1.3257-0.17610.76-1.3140.96932.0496-0.4340.38890.23390.17220.9249-0.11350.664931.0654-38.51824.2964
104.39721.96490.743116.58252.48390.72620.7458-1.22110.16550.6008-0.90150.07890.0554-0.1230.15570.2939-0.17040.01350.5190.00460.10363.9308-26.406259.8358
118.06654.36211.02634.3142.8638.94070.6204-0.170.64840.0105-0.2913-0.33370.4854-0.007-0.32910.32630.01940.18640.20830.06980.339811.2084-20.806349.4374
120.5714-0.2485-2.2526.2349-4.390126.81060.0916-0.2042-0.0654-0.00330.15540.72080.6224-0.3822-0.2470.0972-0.14290.03680.2692-0.10550.2553-0.5603-26.876954.805
132.2871.97382.75333.00771.267512.60710.0613-0.45860.12870.5666-0.40240.17720.1089-0.37760.34110.2374-0.02830.04340.1641-0.02170.01773.1697-36.272652.865
145.8725-0.30231.04540.98550.00283.39970.4331-0.4276-0.47770.3781-0.2753-0.14060.5808-0.4045-0.15780.2837-0.1932-0.10820.16030.07990.10928.3161-42.770945.6432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 25
2X-RAY DIFFRACTION2A26 - 53
3X-RAY DIFFRACTION3A54 - 104
4X-RAY DIFFRACTION4A105 - 170
5X-RAY DIFFRACTION5B4 - 57
6X-RAY DIFFRACTION6B58 - 93
7X-RAY DIFFRACTION7B94 - 100
8X-RAY DIFFRACTION8B101 - 167
9X-RAY DIFFRACTION9B168 - 171
10X-RAY DIFFRACTION10C2 - 23
11X-RAY DIFFRACTION11C24 - 48
12X-RAY DIFFRACTION12C49 - 66
13X-RAY DIFFRACTION13C67 - 108
14X-RAY DIFFRACTION14C109 - 170

+
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