[English] 日本語
Yorodumi
- PDB-3aem: Reaction intermediate structure of Entamoeba histolytica methioni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3aem
TitleReaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing Michaelis complex and methionine imine-pyridoxamine-5'-phosphate
Components(Methionine gamma- ...) x 2
KeywordsLYASE / gamma-lyase / L-methionine / entamoeba histolytica
Function / homology
Function and homology information


cystathionine gamma-synthase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2LM / METHIONINE / cystathionine gamma-synthase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKaraki, T. / Sato, D. / Shimizu, A. / Nozaki, T. / Harada, S.
CitationJournal: To be published
Title: Crystal structure of Entamoeba histolytica methionine gamma-lyase 1
Authors: Karaki, T. / Sato, D. / Shimizu, A. / Nozaki, T. / Harada, S.
History
DepositionFeb 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,48414
Polymers169,6314
Non-polymers1,85310
Water16,033890
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19940 Å2
ΔGint-132 kcal/mol
Surface area47670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.086, 85.332, 114.331
Angle α, β, γ (deg.)90.000, 101.900, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Methionine gamma- ... , 2 types, 4 molecules ABDC

#1: Protein Methionine gamma-lyase


Mass: 42350.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: metg / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q86D28, methionine gamma-lyase
#2: Protein Methionine gamma-lyase


Mass: 42578.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: metg / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q86D28, methionine gamma-lyase

-
Non-polymers , 5 types, 900 molecules

#3: Chemical ChemComp-2LM / (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid


Mass: 378.338 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H19N2O7PS
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence details1. ACCORDING TO AUTHOR, THE SUBSTITUTION OF LEU TO SER AT A308, B808, C1308, D1808 ARE ALLELIC ...1. ACCORDING TO AUTHOR, THE SUBSTITUTION OF LEU TO SER AT A308, B808, C1308, D1808 ARE ALLELIC VARIATION. 2. SINCE THE GENE HAD INTERNAL METHIONINE AND UPSTREAM OF THIS MET IS SIMILAR TO SHINE-DALGARNO SEQUENCE, SEVERAL NUCLEOTIDES WERE REPLACED NOT TO CHANGE THE AMINO ACID RESIDUES, BUT AVOID RIBOSOME BINDING IN E. COLI EXPRESSION SYSTEM.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 1.8M (NH4)2SO4, 0.1M cacodylate buffer, 0.1M Li3(C3H5O(COO)3), 0.1mM pyridozxal 5'-phosphate, pH 6.6, vapor diffusion, sitting drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 94891 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.541
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.595 / % possible all: 99.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å48.48 Å
Translation4 Å48.48 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ACZ

3acz


Resolution: 2.2→48.48 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.11 / SU ML: 0.105 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19556 4752 5 %RANDOM
Rwork0.15104 ---
obs0.15323 90121 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.013 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.06 Å2
2--0.09 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11767 0 113 890 12770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02212140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9716424
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84351548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23124.592466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.204152102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4621537
X-RAY DIFFRACTIONr_chiral_restr0.1070.21865
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218939
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6261.57689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.216212379
X-RAY DIFFRACTIONr_scbond_it2.32934451
X-RAY DIFFRACTIONr_scangle_it3.7784.54041
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.197→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 356 -
Rwork0.185 6380 -
obs--96.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6875-0.2437-0.22670.8549-0.10591.5578-0.03490.1863-0.1976-0.08870.02460.06160.2317-0.22740.01020.1879-0.05460.00440.1257-0.04580.150.873-13.8335.242
21.9168-0.029-0.19110.56450.1530.4707-0.00620.09020.1056-0.0233-0.01860.1441-0.0417-0.07420.02490.13820.00040.00090.03880.02080.1534-13.0564.03645.804
31.049-0.1154-0.10631.72270.65090.82830.017-0.04370.18440.0068-0.03460.0803-0.0395-0.09910.01760.12180.01130.00540.0619-0.00280.15812.04318.1557.179
40.74540.10940.09460.747-0.4011.2563-0.01990.2886-0.237-0.17680.0184-0.05070.27180.0460.00150.2334-0.02040.0360.1434-0.08320.135617.752-17.86628.331
51.2472-0.18670.10510.78610.0020.92960.0590.5026-0.0046-0.2458-0.0544-0.16260.05380.1495-0.00470.19490.01320.0920.27-0.03680.063235.835-4.64213.238
61.72170.0822-0.58691.98890.54792.1980.20790.27190.4507-0.2899-0.0491-0.3137-0.38290.2805-0.15880.3128-0.05010.13690.36750.14650.200632.15816.0759.687
70.9218-0.5289-0.32060.6089-0.20132.22260.04730.12930.2298-0.0813-0.0137-0.1339-0.22720.2636-0.03360.1854-0.05670.02890.12220.03590.188724.94714.15334.499
81.8881-0.27520.23250.5894-0.18570.45730.01380.0643-0.0452-0.0259-0.0394-0.12760.03980.05630.02550.1406-0.00450.02260.0341-0.01280.151238.578-3.79845.593
91.0310.04130.18271.7457-0.51030.75670.0307-0.0333-0.18050.0104-0.0281-0.110.03350.0927-0.00260.12520.00890.01950.0649-0.00350.16623.994-18.34357.181
100.7194-0.3558-0.28340.48450.43471.78180.06850.26380.2117-0.1535-0.0287-0.0201-0.249-0.044-0.03990.2191-0.01480.00890.14380.08050.18088.34118.12829.648
111.68320.1389-0.32350.74120.18391.2072-0.02390.58990.1881-0.2060.04720.1549-0.0902-0.2593-0.02330.1754-0.0019-0.06370.30730.11380.0775-12.7187.87617.457
122.07140.22620.29921.44340.63511.7532-0.04160.7413-0.2093-0.28490.03870.11910.1681-0.38030.00290.2551-0.1128-0.03940.5367-0.09360.0415-4.357-10.7557.081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 68
2X-RAY DIFFRACTION2A69 - 251
3X-RAY DIFFRACTION3A252 - 389
4X-RAY DIFFRACTION4B503 - 566
5X-RAY DIFFRACTION5B567 - 806
6X-RAY DIFFRACTION6B807 - 888
7X-RAY DIFFRACTION7C1003 - 1064
8X-RAY DIFFRACTION8C1065 - 1252
9X-RAY DIFFRACTION9C1253 - 1389
10X-RAY DIFFRACTION10D1505 - 1562
11X-RAY DIFFRACTION11D1563 - 1743
12X-RAY DIFFRACTION12D1744 - 1888

+
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