[English] 日本語
Yorodumi
- PDB-7f1v: Crystal structure of Pseudomonas putida methionine gamma-lyase Q3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f1v
TitleCrystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates
Components(L-methionine gamma-lyase) x 2
KeywordsLYASE / Pseudomonas putida / methionine gamma-lyase / PLP enzyme
Function / homology
Function and homology information


homocysteine desulfhydrase activity / homocysteine desulfhydrase / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
L-methionine gamma-lyase / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-7XF / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-methionine gamma-lyase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOkawa, A. / Handa, H. / Yasuda, E. / Murota, M. / Kudo, D. / Tamura, T. / Shiba, T. / Inagaki, K.
CitationJournal: J.Biosci.Bioeng. / Year: 2022
Title: Characterization and application of l-methionine gamma-lyase Q349S mutant enzyme with an enhanced activity toward l-homocysteine.
Authors: Okawa, A. / Handa, H. / Yasuda, E. / Murota, M. / Kudo, D. / Tamura, T. / Shiba, T. / Inagaki, K.
History
DepositionJun 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 13, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-methionine gamma-lyase
B: L-methionine gamma-lyase
C: L-methionine gamma-lyase
D: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8547
Polymers170,9874
Non-polymers8683
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19140 Å2
ΔGint-98 kcal/mol
Surface area45570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.075, 152.299, 80.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein L-methionine gamma-lyase / MGL / Homocysteine desulfhydrase / L-methioninase


Mass: 42632.566 Da / Num. of mol.: 2 / Mutation: Q349S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdeA / Production host: Escherichia coli (E. coli)
References: UniProt: P13254, methionine gamma-lyase, homocysteine desulfhydrase
#2: Protein L-methionine gamma-lyase / MGL / Homocysteine desulfhydrase / L-methioninase


Mass: 42860.684 Da / Num. of mol.: 2 / Mutation: Q349S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdeA / Production host: Escherichia coli (E. coli)
References: UniProt: P13254, methionine gamma-lyase, homocysteine desulfhydrase
#3: Chemical ChemComp-7XF / (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-sulfanyl-butanoic acid


Mass: 366.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NA-K PHOSPHATE BUFFER, pH 5.6-5.8, 6-9 % PEG 6000, 0.25 M AMMONIUM SULFATE. 0.5 MM PLP, 0.5%(v/v) 2-mercaptoethanol
PH range: 5.6-5.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 19, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 90099 / % possible obs: 97.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 6.5
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4248 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7C

2o7c


Resolution: 2.25→19.97 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.208 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22658 3961 5 %RANDOM
Rwork0.18782 ---
obs0.18978 75074 87.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.25→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11849 0 54 198 12101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912161
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211577
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.96716512
X-RAY DIFFRACTIONr_angle_other_deg0.9793.00126544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3951568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59523.32509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.919151882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9611580
X-RAY DIFFRACTIONr_chiral_restr0.0830.21856
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022818
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0083.786293
X-RAY DIFFRACTIONr_mcbond_other2.0083.7796289
X-RAY DIFFRACTIONr_mcangle_it3.3465.667854
X-RAY DIFFRACTIONr_mcangle_other3.3465.6597853
X-RAY DIFFRACTIONr_scbond_it2.0634.0655868
X-RAY DIFFRACTIONr_scbond_other2.0554.0645867
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4495.9958659
X-RAY DIFFRACTIONr_long_range_B_refined5.68729.70712948
X-RAY DIFFRACTIONr_long_range_B_other5.68529.71612922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.254→2.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 207 -
Rwork0.249 3633 -
obs--58.88 %

+
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