[English] 日本語
Yorodumi
- PDB-3lgs: A. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lgs
TitleA. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine
Components5'-methylthioadenosine nucleosidases
KeywordsHYDROLASE
Function / homology
Function and homology information


methylthioadenosine nucleosidase / phloem or xylem histogenesis / methylthioadenosine nucleosidase activity / nucleoside metabolic process / L-methionine salvage from methylthioadenosine / plasma membrane / cytosol
Similarity search - Function
5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / S-ADENOSYL-L-HOMOCYSTEINE / 5'-methylthioadenosine nucleosidase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSiu, K.K.W. / Howell, P.L.
Citation
Journal: J.Struct.Biol. / Year: 2011
Title: Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases.
Authors: Siu, K.K. / Asmus, K. / Zhang, A.N. / Horvatin, C. / Li, S. / Liu, T. / Moffatt, B. / Woods, V.L. / Howell, P.L.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases.
Authors: Siu, K.K. / Lee, J.E. / Sufrin, J.R. / Moffatt, B.A. / McMillan, M. / Cornell, K.A. / Isom, C. / Howell, P.L.
History
DepositionJan 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 nucleosidases
B: 5'-methylthioadenosine nucleosidases
C: 5'-methylthioadenosine nucleosidases
D: 5'-methylthioadenosine nucleosidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,54021
Polymers113,9034
Non-polymers2,63717
Water7,098394
1
A: 5'-methylthioadenosine nucleosidases
B: 5'-methylthioadenosine nucleosidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,30111
Polymers56,9512
Non-polymers1,3499
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-12 kcal/mol
Surface area18850 Å2
MethodPISA
2
C: 5'-methylthioadenosine nucleosidases
D: 5'-methylthioadenosine nucleosidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,23910
Polymers56,9512
Non-polymers1,2878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-7 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.850, 126.410, 83.810
Angle α, β, γ (deg.)90.00, 101.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEASPASPAA31 - 20031 - 200
21PHEPHEASPASPBB31 - 20031 - 200
31PHEPHEASPASPCC31 - 20031 - 200
41PHEPHEASPASPDD31 - 20031 - 200
12ALAALAGLYGLYAA204 - 261204 - 261
22ALAALAGLYGLYBB204 - 261204 - 261
32ALAALAGLYGLYCC204 - 261204 - 261
42ALAALAGLYGLYDD204 - 261204 - 261

-
Components

#1: Protein
5'-methylthioadenosine nucleosidases


Mass: 28475.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g38800, atmtan1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C+
References: UniProt: Q9T0I8, methylthioadenosine nucleosidase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M NH4Cl, 18 % (w/v) PEG 3350, 15 % (v/v) Ethylene glycol, pH 7.5, vapor diffusion, temperature 298K

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: CONFOCAL MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→23.12 Å / Num. obs: 46037 / % possible obs: 97.2 % / Redundancy: 3.78 % / Rmerge(I) obs: 0.084 / Χ2: 0.9 / Net I/σ(I): 7.4 / Scaling rejects: 9154
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.2-2.283.660.33831749544801.0495.2
2.28-2.373.730.2893.51795045440.9996.4
2.37-2.483.760.263.81803245400.9796
2.48-2.613.770.2154.51804445300.9796.5
2.61-2.773.780.1715.41829345830.9596.9
2.77-2.983.780.1376.51841245990.9197.4
2.98-3.283.810.1028.11859246400.8697.4
3.28-3.763.830.07410.91869146540.8398.5
3.76-4.733.850.05813.61886146980.7598.7
4.73-23.123.790.05813.61870647690.7499.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
d*TREK9.9.7Ldata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→23.12 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.439 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26 4627 10.1 %RANDOM
Rwork0.21 ---
obs0.21 45991 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.14 Å2 / Biso mean: 22.686 Å2 / Biso min: 3.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.8 Å2
2---0.69 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7347 0 144 394 7885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227759
X-RAY DIFFRACTIONr_angle_refined_deg1.3392.00510599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70251023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22625.298285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.631151284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9241531
X-RAY DIFFRACTIONr_chiral_restr0.0830.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215707
X-RAY DIFFRACTIONr_mcbond_it0.4771.54958
X-RAY DIFFRACTIONr_mcangle_it0.87328058
X-RAY DIFFRACTIONr_scbond_it1.34632801
X-RAY DIFFRACTIONr_scangle_it2.1884.52522
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A893MEDIUM POSITIONAL0.170.5
2B893MEDIUM POSITIONAL0.210.5
3C893MEDIUM POSITIONAL0.230.5
4D893MEDIUM POSITIONAL0.20.5
1A746LOOSE POSITIONAL0.495
2B746LOOSE POSITIONAL0.545
3C746LOOSE POSITIONAL0.585
4D746LOOSE POSITIONAL0.525
1A893MEDIUM THERMAL0.522
2B893MEDIUM THERMAL0.582
3C893MEDIUM THERMAL0.632
4D893MEDIUM THERMAL0.562
1A746LOOSE THERMAL0.7110
2B746LOOSE THERMAL0.7210
3C746LOOSE THERMAL0.7310
4D746LOOSE THERMAL0.7210
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 310 -
Rwork0.298 3000 -
all-3310 -
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