[English] 日本語
Yorodumi
- PDB-3rw9: Crystal Structure of human Spermidine Synthase in Complex with de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rw9
TitleCrystal Structure of human Spermidine Synthase in Complex with decarboxylated S-adenosylhomocysteine
ComponentsSpermidine synthase
KeywordsTRANSFERASE / aminopropyltransferase
Function / homology
Function and homology information


Metabolism of polyamines / polyamine metabolic process / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cellular response to leukemia inhibitory factor / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Spermidine/spermine synthase, eukaryotes / 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. ...Spermidine/spermine synthase, eukaryotes / 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
5'-S-(3-aminopropyl)-5'-thioadenosine / Spermidine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeckute, J. / McCloskey, D.E. / Thomas, H.J. / Secrist III, J.A. / Pegg, A.E. / Ealick, S.E.
CitationJournal: Protein Sci. / Year: 2011
Title: Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine.
Authors: Seckute, J. / McCloskey, D.E. / Thomas, H.J. / Secrist, J.A. / Pegg, A.E. / Ealick, S.E.
History
DepositionMay 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7864
Polymers68,1062
Non-polymers6812
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-15 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.177, 60.816, 87.021
Angle α, β, γ (deg.)90.000, 108.050, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN B AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...B18 - 42
121CHAIN B AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...B44 - 94
131CHAIN B AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...B96 - 175
141CHAIN B AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...B178 - 185
151CHAIN B AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...B187 - 299
161CHAIN B AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...B401
211CHAIN A AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...A18 - 42
221CHAIN A AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...A44 - 94
231CHAIN A AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...A96 - 175
241CHAIN A AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...A178 - 185
251CHAIN A AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...A187 - 299
261CHAIN A AND (RESSEQ 18:42 OR RESSEQ 44:94 OR RESSEQ...A401

-
Components

#1: Protein Spermidine synthase / / SPDSY / Putrescine aminopropyltransferase


Mass: 34052.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRM, SPS1, SRML1 / Plasmid: modified pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19623, spermidine synthase
#2: Chemical ChemComp-DSH / 5'-S-(3-aminopropyl)-5'-thioadenosine


Mass: 340.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N6O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 20% PEG 3350, 0.2 M sodium sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33549 / Observed criterion σ(I): -3

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.56 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 0.04 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 1694 5.05 %RANDOM
Rwork0.2109 ---
obs0.2134 33549 85.53 %-
all-89877 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.651 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 73.33 Å2 / Biso mean: 20.8277 Å2 / Biso min: 3.96 Å2
Baniso -1Baniso -2Baniso -3
1-9.5995 Å2-0 Å2-3.6879 Å2
2---7.5062 Å2-0 Å2
3----2.0932 Å2
Refinement stepCycle: LAST / Resolution: 2→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 46 407 4861
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2155X-RAY DIFFRACTIONPOSITIONAL0.031
12A2155X-RAY DIFFRACTIONPOSITIONAL0.031

+
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