[English] 日本語
Yorodumi
- PDB-1qm4: Methionine Adenosyltransferase Complexed with a L-Methionine Analogue -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qm4
TitleMethionine Adenosyltransferase Complexed with a L-Methionine Analogue
ComponentsMETHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
KeywordsTRANSFERASE / ADENOSYLTRANSFERASE / METHIONINE BINDING
Function / homology
Function and homology information


Metabolism of ingested SeMet, Sec, MeSec into H2Se / Sulfur amino acid metabolism / L-methionine catabolic process / methionine adenosyltransferase complex / Methylation / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / amino acid binding / one-carbon metabolic process ...Metabolism of ingested SeMet, Sec, MeSec into H2Se / Sulfur amino acid metabolism / L-methionine catabolic process / methionine adenosyltransferase complex / Methylation / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / amino acid binding / one-carbon metabolic process / ADP binding / nuclear matrix / protein-containing complex assembly / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #10 / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain ...GMP Synthetase; Chain A, domain 3 - #10 / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2. / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-2-AMINO-4-METHOXY-CIS-BUT-3-ENOIC ACID / : / S-adenosylmethionine synthase isoform type-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsGonzalez, B. / Pajares, M.A. / Hermoso, J.A. / Sanz-Aparicio, J.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Crystal Structure of Tetrameric Methionine Adenosyltransferase from Rat Liver Reveals the Methionine-Binding Site
Authors: Gonzalez, B. / Pajares, M.A. / Hermoso, J.A. / Alvarez, L. / Garrido, F. / Sufrin, J.R. / Sanz-Aparicio, J.
#1: Journal: Biochem.J. / Year: 1994
Title: Expression of Rat Liver S-Adenosylmethionine Synthetase in Escherichia Coli Results in Two Active Oligomeric Forms
Authors: Alvarez, L. / Mingorance, J. / Pajares, M.A. / Mato, J.M.
History
DepositionSep 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4May 30, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.5Dec 13, 2023Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
B: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,86111
Polymers87,2752
Non-polymers5859
Water3,549197
1
A: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
B: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
hetero molecules

A: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
B: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,72122
Polymers174,5514
Non-polymers1,17018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+3/41
Buried area12050 Å2
ΔGint-82.7 kcal/mol
Surface area61270 Å2
MethodPQS
Unit cell
Length a, b, c (Å)115.200, 115.200, 159.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.78343, -0.23114, 0.5769), (-0.21651, -0.76861, -0.60197), (0.58255, -0.59651, 0.5521)
Vector: 0.0983, 0.70748, 0.16955)
DetailsTHE ENZYME IS A TETRAMERTHE DIMER IN THE ASYMMETRIC UNIT HAS A PROTEIN PROTEININTERACTION ABOUT THE LARGEST FACE OF THE MONOMERICMOLECULE AND THE TETRAMER IS MADE UP OF TWO OF THESEDIMERS INTERACTING IN A 'HEAD-TO-HEAD' MANNER .IN THE CRYSTAL THE DIMER MOLECULES ARE INVOLVED IN A STRONGCRYSTAL PACKING INTERACTION INVOLVING THE OPPOSITE FACEOF THE MOLECULES TO THAT INVOLVED IN THE BIOLOGICAL DIMER.FOR EXAMPLE SYMMETRY OPERATION,BIOMT1 2 1.000000 0.000000 0. 000000 0.00000BIOMT2 2 0.000000 -1.000000 0.000000 115.20000BIOMT3 2 0.000000 0. 000000 -1.000000 79.99000GENERATES A CRYSTAL PACKING TETRAMERIC ASSEMBLY.

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM / ADOMET SYNTHETASE / MAT-I / S-ADENOSYLMETHIONINE SYNTHETASE


Mass: 43637.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: LIVER / Plasmid: PSSRL-T7N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13444, methionine adenosyltransferase

-
Non-polymers , 5 types, 206 molecules

#2: Chemical ChemComp-AMB / L-2-AMINO-4-METHOXY-CIS-BUT-3-ENOIC ACID


Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growpH: 7.5
Details: 16 % PEG 10K, 10MM CIS-AMB, 0.1 HEPES PH=7.5, pH 7.50
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Details: drop consists of equal amounts of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlprotein1drop
250 mMTris-HCl1drop
310 mML-cisAMB1drop
410 mMdithiothreitol1drop
550 mM1dropKCl
610 mM1dropMgSO4
71 mMEDTA1drop
816 %(w/v)PEG100001reservoirprecipitant
9100 mMHEPES1reservoirprecipitant

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.66→44.7 Å / Num. obs: 28742 / % possible obs: 94.5 % / Observed criterion σ(I): 4 / Redundancy: 7.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 6.7
Reflection shellResolution: 2.66→2.8 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.37 / % possible all: 85.8
Reflection shell
*PLUS
% possible obs: 85.8 % / Rmerge(I) obs: 0.37

-
Processing

Software
NameVersionClassification
X-PLOR3.843refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MXA

1mxa


Resolution: 2.66→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: NO DENSITY FOR RESIDUES A1-A16, AND B1-B16, WAS OBSERVED IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 -7 %RANDOM
Rwork0.23 ---
obs0.23 28276 84.3 %-
Displacement parametersBiso mean: 41.5 Å2
Refinement stepCycle: LAST / Resolution: 2.66→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5692 0 29 197 5918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.03
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: 2.66→2.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.34 -7 %
Rwork0.28 3100 -
obs--70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTIOH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.03

+
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