[English] 日本語
Yorodumi
- PDB-1jdt: CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLAS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jdt
TitleCRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH MTA AND SULFATE ION
Components5'-METHYLTHIOADENOSINE PHOSPHORYLASE
KeywordsTRANSFERASE / alpha-beta protein
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / nucleoside catabolic process / purine-nucleoside phosphorylase / cytosol
Similarity search - Function
Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAppleby, T.C. / Mathews, I.I. / Porcelli, M. / Cacciapuoti, G. / Ealick, S.E.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus.
Authors: Appleby, T.C. / Mathews, I.I. / Porcelli, M. / Cacciapuoti, G. / Ealick, S.E.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Purification and characterization of extremely thermophilic and thermostable 5'-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus. Purine nucleoside phosphorylase ...Title: Purification and characterization of extremely thermophilic and thermostable 5'-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus. Purine nucleoside phosphorylase activity and evidence for intersubunit disulfide bonds
Authors: Cacciapuoti, G. / Porcelli, M. / Bertoldo, C. / De Rosa, M. / Zappia, V.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Three-Dimensional Structure of Human Erythrocytic Purine Nucleoside Phosphorylase At 3.2 Resolution
Authors: Ealick, S.E. / Rule, S.A. / Carter, D.C. / Greenhough, T.J. / Babu, Y.S.
#3: Journal: Structure / Year: 1999
Title: The structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase at 1.7 resolution provides insights into substrate binding and catalysis
Authors: Appleby, T.C. / Erion, M.D. / Ealick, S.E.
History
DepositionJun 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...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 / 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: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
B: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
C: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4719
Polymers77,2903
Non-polymers1,1806
Water3,009167
1
A: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
B: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
C: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
hetero molecules

A: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
B: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
C: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,94118
Polymers154,5816
Non-polymers2,36012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area21860 Å2
ΔGint-201 kcal/mol
Surface area45900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.6, 176.3, 87.1
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Detailshexamer generated from the trimer in the asymmetric unit by the crystallographic two fold

-
Components

#1: Protein 5'-METHYLTHIOADENOSINE PHOSPHORYLASE / E.C.2.4.2.28 / MTA PHOSPHORYLASE / MTAP


Mass: 25763.457 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: P50389, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: dioxane, MPD, MgCl2, NaCl, Tris.HCl at pH 7.4, VAPOR DIFFUSION, HANGING DROP, 291K
Crystal grow
*PLUS
Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-10 mg/mlprotein1drop
228-30 %dioxane1reservoir
312 %MPD1reservoir
40.12 M1reservoirMgCl2
50.04 M1reservoirNaCl
60.1 MTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9023 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9023 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 50489 / Num. obs: 50489 / % possible obs: 95.2 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.1
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.5 / % possible all: 79.2
Reflection
*PLUS
Num. measured all: 213837
Reflection shell
*PLUS
% possible obs: 72 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native SsMTAP

Resolution: 2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2510 5 %Random
Rwork0.222 ---
all-50415 --
obs-50045 --
Displacement parametersBiso mean: 34.7 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5286 0 75 167 5528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.257
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.7 Å2

+
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