[English] 日本語
Yorodumi
- PDB-6hy1: Plasmodium falciparum spermidine synthase in complex with 5'-meth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hy1
TitlePlasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal
ComponentsSpermidine synthase
KeywordsTRANSFERASE / Inhibitor complex / catalysis / kinetics
Function / homology
Function and homology information


Metabolism of polyamines / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / cytosol
Similarity search - Function
Spermidine synthase, tetramerisation domain / Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain ...Spermidine synthase, tetramerisation domain / Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain / Spermidine Synthase; Chain: A, domain 2 / Vaccinia Virus protein VP39 / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine / trans-N-(3-aminopropyl)cyclohexane-1,4-diamine / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Spermidine synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSprenger, J. / Coertzen, D. / Persson, L. / Carey, J. / Birkholtz, L.M. / Louw, B.I.
CitationJournal: To Be Published
Title: Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal
Authors: Sprenger, J. / Coertzen, D. / Persson, L. / Carey, J. / Birkholtz, L.M. / Louw, B.I.
History
DepositionOct 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spermidine synthase
B: Spermidine synthase
C: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,90018
Polymers96,2313
Non-polymers2,66915
Water14,124784
1
A: Spermidine synthase
hetero molecules

A: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,89410
Polymers64,1542
Non-polymers1,7408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6270 Å2
ΔGint-3 kcal/mol
Surface area20990 Å2
MethodPISA
2
B: Spermidine synthase
C: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,95313
Polymers64,1542
Non-polymers1,79911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-19 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.870, 135.000, 48.570
Angle α, β, γ (deg.)90.00, 95.95, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Spermidine synthase /


Mass: 32077.021 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1129000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8II73, spermidine synthase

-
Non-polymers , 6 types, 799 molecules

#2: Chemical ChemComp-GXQ / N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine


Mass: 228.378 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C12H28N4
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / Polyethylene glycol


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-JFQ / trans-N-(3-aminopropyl)cyclohexane-1,4-diamine


Mass: 171.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H21N3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 3350, 0.1M ammonium sulfate, 0.1M 2-(N-morpholino) ethanesulfonic acid, pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9299 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9299 Å / Relative weight: 1
ReflectionResolution: 1.55→111.68 Å / Num. obs: 175421 / % possible obs: 94.3 % / Redundancy: 6.833 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 1.075 / Net I/σ(I): 16.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.594.9551.6370.8771880.431.82852.4
1.59-1.636.7281.2371.47123170.6871.3491.5
1.63-1.687.211.031.88125940.8141.10996.8
1.68-1.737.1530.7852.47122810.8830.84697.3
1.73-1.797.0480.5743.28119120.9250.61997.5
1.79-1.856.6460.4284.18115840.9480.46597.8
1.85-1.927.0870.3095.89111620.9770.33497.8
1.92-27.2250.2347.99108030.9860.25298
2-2.097.1070.17110.46103720.9920.18498.1
2.09-2.196.8830.12413.6699370.9950.13498.5
2.19-2.316.5520.10515.7694780.9960.11598.4
2.31-2.457.2350.08320.5389660.9980.08998.7
2.45-2.616.9870.07223.5684110.9980.07898.7
2.61-2.826.7810.05728.8978930.9980.06298.8
2.82-3.096.6750.04435.9772750.9990.04899.2
3.09-3.466.8640.03644.9766020.9990.03999.3
3.46-3.996.5220.0352.6957910.9990.03299.1
3.99-4.896.2860.02556.949310.9990.02799.2
4.89-6.926.7420.02457.9838210.9990.02699.2
6.92-111.686.4820.01962.08210310.02198.5

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→32.167 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 8308 5.05 %RANDOM
Rwork0.1757 ---
obs0.177 164672 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→32.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 180 784 7713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147075
X-RAY DIFFRACTIONf_angle_d1.2329532
X-RAY DIFFRACTIONf_dihedral_angle_d14.8864203
X-RAY DIFFRACTIONf_chiral_restr0.0861057
X-RAY DIFFRACTIONf_plane_restr0.0091168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.43922630.39064949X-RAY DIFFRACTION93
1.6182-1.63720.39822690.34935084X-RAY DIFFRACTION96
1.6372-1.65720.32142770.33125124X-RAY DIFFRACTION97
1.6572-1.67820.33062790.30275221X-RAY DIFFRACTION97
1.6782-1.70020.2793050.28625090X-RAY DIFFRACTION97
1.7002-1.72350.30462810.26825157X-RAY DIFFRACTION97
1.7235-1.74820.2682740.25485161X-RAY DIFFRACTION97
1.7482-1.77420.28322810.24365158X-RAY DIFFRACTION97
1.7742-1.8020.25032520.23825241X-RAY DIFFRACTION97
1.802-1.83150.26522810.23815138X-RAY DIFFRACTION98
1.8315-1.86310.26052400.22955222X-RAY DIFFRACTION97
1.8631-1.8970.24122690.21235161X-RAY DIFFRACTION98
1.897-1.93340.22492630.20095235X-RAY DIFFRACTION98
1.9334-1.97290.22492650.19965201X-RAY DIFFRACTION98
1.9729-2.01580.25342860.19555237X-RAY DIFFRACTION98
2.0158-2.06270.20052880.18515182X-RAY DIFFRACTION98
2.0627-2.11430.22082690.17955302X-RAY DIFFRACTION98
2.1143-2.17140.21162740.18355159X-RAY DIFFRACTION98
2.1714-2.23530.22172850.19125247X-RAY DIFFRACTION98
2.2353-2.30740.22532640.18875278X-RAY DIFFRACTION98
2.3074-2.38990.19542850.17575205X-RAY DIFFRACTION99
2.3899-2.48550.20112890.17945226X-RAY DIFFRACTION99
2.4855-2.59860.21312780.17445292X-RAY DIFFRACTION99
2.5986-2.73550.19492740.1755262X-RAY DIFFRACTION99
2.7355-2.90680.20322780.16755259X-RAY DIFFRACTION99
2.9068-3.13110.18332890.17065294X-RAY DIFFRACTION99
3.1311-3.44580.20012800.1715314X-RAY DIFFRACTION99
3.4458-3.94370.16813040.14915271X-RAY DIFFRACTION99
3.9437-4.96570.1462480.12965355X-RAY DIFFRACTION99
4.9657-32.1730.17263180.15065339X-RAY DIFFRACTION99

+
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