[English] 日本語
Yorodumi
- PDB-1cg6: STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cg6
TitleSTRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE AND SULFATE AT 1.7 A RESOLUTION
ComponentsPROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
KeywordsTRANSFERASE / METHYLTHIOADENOSINE PHOSPHORYLASE / PURINE NUCLEOSIDE PHOSPHORYLASE / PURINE SALVAGE / METHYLTHIOADENOSINE / SULFATE
Function / homology
Function and homology information


Methionine salvage pathway / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation ...Methionine salvage pathway / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 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 / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsAppleby, T.C. / Erion, M.D. / Ealick, S.E.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase at 1.7 A resolution provides insights into substrate binding and catalysis.
Authors: Appleby, T.C. / Erion, M.D. / Ealick, S.E.
History
DepositionMar 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: 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: PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6703
Polymers31,2771
Non-polymers3932
Water2,756153
1
A: PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
hetero molecules

A: PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
hetero molecules

A: PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0119
Polymers93,8313
Non-polymers1,1806
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9350 Å2
ΔGint-122 kcal/mol
Surface area30010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.830, 122.830, 45.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Cell settingtrigonal
Space group name H-MP321

-
Components

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


Mass: 31277.053 Da / Num. of mol.: 1 / Mutation: ILE56VAL
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE AND SULFATE
Source: (gene. exp.) Homo sapiens (human) / Tissue: PLACENTA
Description: MTAP CDNA WAS ISOLATED FROM A HUMAN PLACENTA CDNA LIBRARY AND EXPRESSED IN E. COLI
Cellular location: CYTOPLASM / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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 Å3/Da / Density % sol: 59 %
Crystal growpH: 7.4
Details: 12% (W/V) PEG 6000, 25% (V/V) ETHYLENE GLYCOL, 0.2M TRIS-HCL PH 7.8, 0.002M DTT, pH 7.4
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG80001drop
20.1 MHEPES1drop
38 %ethylene glycol1drop
412 %(w/v)PEG60001reservoir
525 %(v/v)ethylene glycol1reservoir
6200 mMTris-HCl1reservoir
72 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.919
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 42292 / % possible obs: 96.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 5.3 / Net I/σ(I): 9.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6 % / Mean I/σ(I) obs: 6.5 / Rsym value: 10.6 / % possible all: 93.2
Reflection
*PLUS
Num. measured all: 393633 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.106

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.7→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4174 10.1 %RANDOM
Rwork0.202 ---
obs-41325 96.6 %-
Displacement parametersBiso mean: 21.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.218 Å0.2 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 25 153 2244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.249
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.299 467 9.6 %
Rwork0.287 4388 -
obs--92.6 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor Rfree: 0.299 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.287

+
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