[English] 日本語
Yorodumi
- PDB-1m6e: CRYSTAL STRUCTURE OF SALICYLIC ACID CARBOXYL METHYLTRANSFERASE (SAMT) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m6e
TitleCRYSTAL STRUCTURE OF SALICYLIC ACID CARBOXYL METHYLTRANSFERASE (SAMT)
ComponentsS-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase
KeywordsTRANSFERASE / Rossmann fold / protein-small molecule complex
Function / homology
Function and homology information


salicylate 1-O-methyltransferase / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Methyltransferase, alpha-helical capping domain / Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / SAM dependent carboxyl methyltransferase / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Methyltransferase, alpha-helical capping domain / Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / SAM dependent carboxyl methyltransferase / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / 2-HYDROXYBENZOIC ACID / Salicylate carboxymethyltransferase
Similarity search - Component
Biological speciesClarkia breweri (fairy fans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsZubieta, C. / Ross, J.R. / Koscheski, P. / Yang, Y. / Pichersky, E. / Noel, J.P.
CitationJournal: Plant Cell / Year: 2003
Title: Structural Basis for Substrate Recognition in The Salicylic Acid Carboxyl Methyltransferase Family
Authors: Zubieta, C. / Ross, J.R. / Koscheski, P. / Yang, Y. / Pichersky, E. / Noel, J.P.
History
DepositionJul 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
X: S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0294
Polymers40,3311
Non-polymers6973
Water25214
1
X: S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase
hetero molecules

X: S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0578
Polymers80,6622
Non-polymers1,3956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)141.740, 141.740, 63.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsthe biological assembly is a dimer formed by y,x,1-z

-
Components

#1: Protein S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase


Mass: 40331.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clarkia breweri (fairy fans) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SPV4
#2: Chemical ChemComp-LU / LUTETIUM (III) ION / LU / Lutetium


Mass: 174.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Lu
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.0-2.2 Mammonium sulfate1reservoir
20.5 mMSA1reservoir
30.05 M3-(N-morpholino)-propanesulfonic acid-Na+1reservoirpH7.5
450 mMTris-HCl1droppH7.5
5100 mM1dropKCl
65 mMbeta-mercaptoethanol1drop
78 mg/mlprotein1drop

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1801
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.6983,1.3407,1.3411
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111) sagitally focusedSINGLE WAVELENGTHMx-ray1
2Si (111) sagitally focusedMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.69831
21.34071
31.34111
ReflectionResolution: 2.9→24.81 Å / Num. all: 13537 / Num. obs: 13537 / % possible obs: 100 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): -3 / Biso Wilson estimate: 66.7 Å2
Reflection shellResolution: 3→3.19 Å / Num. unique all: 2086 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 99 Å / Num. obs: 27353 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.427

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 3→24.81 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 4214998.49 / Data cutoff high rms absF: 4214998.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 673 5 %random
Rwork0.2253 ---
all-13537 --
obs-13537 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.7732 Å2 / ksol: 0.276532 e/Å3
Displacement parametersBiso mean: 66.7 Å2
Baniso -1Baniso -2Baniso -3
1--13.59 Å20 Å20 Å2
2---26.87 Å20 Å2
3---40.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 37 14 2877
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.44
X-RAY DIFFRACTIONc_mcbond_it6.371.5
X-RAY DIFFRACTIONc_mcangle_it9.992
X-RAY DIFFRACTIONc_scbond_it8.852
X-RAY DIFFRACTIONc_scangle_it11.962.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 133 -
Rwork0.328 --
obs-2086 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2sah_para.txtsah_topo.txt
X-RAY DIFFRACTION3sal_para.txtsal_topo.txt
X-RAY DIFFRACTION4lu_para.txtlu_topo.txt
X-RAY DIFFRACTION5water.paramwater.top
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 99 Å / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.44

+
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