[English] 日本語
Yorodumi
- PDB-2pt6: The structure of Plasmodium falciparum spermidine synthase in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pt6
TitleThe structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine
ComponentsSpermidine synthase
KeywordsTRANSFERASE / SPERMIDINE SYNTHASE / STRUCTURAL GENOMICS CONSORTIUM / SGC / dcAdoMet complex
Function / homology
Function and homology information


Metabolism of polyamines / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / 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 / Chem-S4M / Spermidine synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDufe, V.T. / Qiu, W. / Muller, I.B. / Hui, R. / Walter, R.D. / Al-Karadaghi, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO.
Authors: Dufe, V.T. / Qiu, W. / Muller, I.B. / Hui, R. / Walter, R.D. / Al-Karadaghi, S.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Advisory / Data collection / Structure summary
Category: audit_author / diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)111,77211
Polymers109,9213
Non-polymers1,8508
Water7,260403
1
A: Spermidine synthase
hetero molecules

A: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6838
Polymers73,2812
Non-polymers1,4026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4930 Å2
ΔGint0.8 kcal/mol
Surface area21970 Å2
MethodPISA
2
B: Spermidine synthase
C: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4307
Polymers73,2812
Non-polymers1,1495
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-18.4 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.300, 134.180, 48.320
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-701-

1PG

21A-709-

HOH

DetailsThe biological unit is a dimer (chains B & C)

-
Components

#1: Protein Spermidine synthase /


Mass: 36640.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF11_0301 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-ROSETTA OXFORD / References: UniProt: Q8II73, spermidine synthase
#2: Chemical ChemComp-S4M / 5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE


Mass: 356.444 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H24N6O3S
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.1 M Ammonium Sulphate and 0.1 M Bis-Tris, 2.5 mM dcAdoMet, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2006 / Details: mirrors
RadiationMonochromator: Bent silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 80780 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.22 % / Biso Wilson estimate: 30.07 Å2 / Rmerge(I) obs: 0.72 / Rsym value: 0.115 / Net I/σ(I): 13.67
Reflection shellResolution: 2→2.051 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 5.25 / Num. unique all: 38389 / Rsym value: 29.3 / % possible all: 100

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å19.99 Å
Translation2.5 Å19.99 Å

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
REFMAC5.2.0019refinement
REFMAC5.2.0019refinement
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I7C

2i7c


Resolution: 2→19.99 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.715 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21407 4178 5 %RANDOM
Rwork0.18048 ---
all0.18217 ---
obs0.18217 79372 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.935 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å2-2.02 Å2
2---2.22 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6753 0 124 403 7280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227039
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9849503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985845
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79925.729295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.351151282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.677156
X-RAY DIFFRACTIONr_chiral_restr0.0910.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025123
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.23268
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24895
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2548
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8231.54338
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35826850
X-RAY DIFFRACTIONr_scbond_it2.00633134
X-RAY DIFFRACTIONr_scangle_it3.1254.52650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 305 -
Rwork0.25 5793 -
obs--100 %

+
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