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Basic information

Entry
Database: PDB / ID: 3aep
TitleReaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing alpha-amino-alpha, beta-butenoic acid-pyridoxal-5'-phosphate
ComponentsMethionine gamma-lyase
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-4LM / METHANETHIOL / cystathionine gamma-synthase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)171,38916
Polymers169,4034
Non-polymers1,98612
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19890 Å2
ΔGint-135 kcal/mol
Surface area48010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.215, 85.359, 114.649
Angle α, β, γ (deg.)90.000, 101.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Methionine gamma-lyase


Mass: 42350.785 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 706 molecules

#2: Chemical
ChemComp-4LM / (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid


Mass: 330.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15N2O7P
#3: Chemical ChemComp-MEE / METHANETHIOL


Mass: 48.107 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O

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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.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.12 % / Mosaicity: 0.726 °
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: May 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 85091 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.092 / Χ2: 1.045 / Net I/σ(I): 9.529
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1.953 / Num. unique all: 8424 / Χ2: 1.099 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.43 Å42.68 Å
Translation2.43 Å42.68 Å

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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: 2.28→39.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.165 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.88 / SU B: 11.194 / SU ML: 0.122 / SU R Cruickshank DPI: 0.234 / SU Rfree: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.198 4257 5 %RANDOM
Rwork0.156 ---
obs0.158 84948 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.09 Å2 / Biso mean: 32.156 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.01 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.28→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11752 0 124 694 12570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212174
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.97416475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81351548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36124.624465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.084152100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6881536
X-RAY DIFFRACTIONr_chiral_restr0.1070.21864
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218986
X-RAY DIFFRACTIONr_mcbond_it0.651.57702
X-RAY DIFFRACTIONr_mcangle_it1.261212397
X-RAY DIFFRACTIONr_scbond_it2.34634472
X-RAY DIFFRACTIONr_scangle_it3.7634.54072
LS refinement shellResolution: 2.281→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 306 -
Rwork0.245 5633 -
all-5939 -
obs-5939 94.36 %
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)
11.0826-0.1340.21730.51730.26991.77290.01880.2062-0.2407-0.0493-0.00030.05550.2634-0.2733-0.01850.1758-0.0597-0.00770.118-0.03770.11451.01-15.06434.536
21.7916-0.0483-0.12470.63870.16770.5206-0.01670.09440.0839-0.0426-0.0050.1289-0.0244-0.04540.02170.1239-0.0037-0.01820.06310.01850.149-12.2363.10645.416
31.05520.00710.02531.41660.61370.82560.0159-0.04250.19220.0022-0.01320.0519-0.0164-0.0776-0.00270.12230.0123-0.00510.0792-0.00590.16141.90618.07457.353
40.44540.00720.13361.0663-1.2871.7614-0.02680.2706-0.1889-0.22920.0146-0.0670.3840.02950.01220.2266-0.02860.02770.177-0.11340.144214.662-17.82326.919
51.6750.0032-0.02880.6198-0.02521.05420.00090.3975-0.1215-0.1708-0.0116-0.15910.10530.10540.01070.15260.0160.0610.1766-0.07210.084135.854-8.91519.022
62.1123-0.2139-0.2842.1839-0.15011.92190.18580.58440.3962-0.4058-0.0976-0.3568-0.24290.1493-0.08820.2816-0.01050.11770.39980.14530.133331.31311.735.909
71.1263-0.3627-0.74560.3675-0.22622.32650.13110.09230.2757-0.0274-0.0335-0.081-0.28680.3286-0.09770.2046-0.05780.00450.15780.04180.205624.13615.68635.498
81.4884-0.21540.22180.6572-0.23920.51640.00810.0667-0.0167-0.0358-0.0439-0.14920.0350.02830.03580.1258-0.00630.0090.0565-0.01960.165437.796-2.83844.698
91.1022-0.19110.19311.6009-0.53250.9290.0236-0.0302-0.1868-0.0034-0.0195-0.0842-0.00580.0719-0.00410.10940.00490.00080.06930.00210.176523.921-18.25157.296
100.7197-0.543-1.05221.1271.48543.02810.07940.31650.1946-0.2592-0.108-0.0233-0.3755-0.19430.02860.22770.0012-0.03510.21290.10680.169111.01617.51527.493
111.50480.2566-0.27460.77710.0780.9688-0.03850.52490.1991-0.2220.07750.1412-0.0981-0.1719-0.03890.1599-0.0088-0.06550.27620.11460.0748-9.6388.60718.872
122.7356-0.1606-0.06971.71570.69062.8697-0.13040.8098-0.3266-0.32020.09180.14250.2406-0.4670.03860.2808-0.1578-0.06110.5832-0.13340.078-6.21-12.5316.044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 55
2X-RAY DIFFRACTION2A56 - 251
3X-RAY DIFFRACTION3A252 - 389
4X-RAY DIFFRACTION4B503 - 543
5X-RAY DIFFRACTION5B544 - 754
6X-RAY DIFFRACTION6B755 - 888
7X-RAY DIFFRACTION7C1003 - 1050
8X-RAY DIFFRACTION8C1051 - 1251
9X-RAY DIFFRACTION9C1252 - 1389
10X-RAY DIFFRACTION10D1505 - 1543
11X-RAY DIFFRACTION11D1544 - 1760
12X-RAY DIFFRACTION12D1761 - 1888

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