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- PDB-3so4: Methionine-adenosyltransferase from Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 3so4
TitleMethionine-adenosyltransferase from Entamoeba histolytica
ComponentsMethionine-adenosyltransferase
KeywordsTRANSFERASE / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP / S-adenosylmethionine synthetase / PSI / Protein Structure Initiative
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / ATP binding / metal ion 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
ACETATE ION / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.18 Å
AuthorsMerritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: To be Published
Title: Methionine-adenosyltransferase from Entamoeba histolytica
Authors: Merritt, E.A. / Arakaki, T. / Zhang, L. / Napuli, A. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Zucker, F. / Verlinde, C.L.M.J. / Hol, W.G.J.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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-adenosyltransferase
B: Methionine-adenosyltransferase
C: Methionine-adenosyltransferase
D: Methionine-adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,9448
Polymers182,7084
Non-polymers2364
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13930 Å2
ΔGint-58 kcal/mol
Surface area48720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.492, 113.161, 220.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTetramer

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Components

#1: Protein
Methionine-adenosyltransferase / S-adenosylmethionine synthase


Mass: 45677.023 Da / Num. of mol.: 4 / Fragment: residues 4-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: 103.m00148, EHI_174250 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: C4M272, methionine adenosyltransferase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2
Details: protein buffer 25 mM HEPES pH 7.5, 500 mM NaCl; crystallization buffer 400 mM Ammonium Acetate, 100 mM BisTris pH 6.2, 33% PEG 3350, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorDetector: CCD / Date: May 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 23472 / % possible obs: 92.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.171 / Χ2: 1.106 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.272.50.7169420.999156
3.27-3.362.80.76211171.009168.5
3.36-3.452.90.59212921.004177.2
3.45-3.553.10.57314801.088189
3.55-3.663.40.48816101.043195.3
3.66-3.793.70.3616241.097198.1
3.79-3.953.90.37716751.077199.8
3.95-4.134.10.30116821.1211100
4.13-4.344.10.24216621.0951100
4.34-4.614.10.16917051.151100
4.61-4.974.20.16417121.1381100
4.97-5.474.20.14416921.114199.9
5.47-6.264.20.15517161.111199.9
6.26-7.884.20.09917501.115199.7
7.88-5040.0418131.196197

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→50 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.871 / WRfactor Rfree: 0.2386 / WRfactor Rwork: 0.1919 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7982 / SU B: 75.438 / SU ML: 0.562 / SU R Cruickshank DPI: 0.5531 / SU Rfree: 0.6828 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.683 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 1189 5.1 %RANDOM
Rwork0.2278 ---
obs0.2306 23302 91.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.96 Å2 / Biso mean: 80.1164 Å2 / Biso min: 24.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2--2.19 Å20 Å2
3----3.61 Å2
Refinement stepCycle: LAST / Resolution: 3.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11478 0 16 4 11498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211714
X-RAY DIFFRACTIONr_bond_other_d0.0050.027811
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.94315802
X-RAY DIFFRACTIONr_angle_other_deg1.349319159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52251508
X-RAY DIFFRACTIONr_chiral_restr0.0660.21803
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212836
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022232
LS refinement shellResolution: 3.178→3.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 43 -
Rwork0.386 830 -
all-873 -
obs--48.69 %
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)
11.2946-0.0905-0.08361.83130.15790.80550.09260.04280.09830.1923-0.1031-0.27050.01390.05410.01050.2010.0002-0.03270.22780.07240.078825.614-5.751-12.21
20.88130.23420.28091.86510.09041.3115-0.00260.37910.2265-0.0891-0.02740.0881-0.09960.03720.030.18630.0570.05490.34210.1310.08069.2191.405-28.581
30.5568-0.0023-0.45131.99580.24391.682-0.24330.1325-0.29410.0589-0.13710.18490.3876-0.09410.38040.3467-0.01230.18530.2174-0.1310.20931.916-55.03-28.381
41.25050.4090.04922.38550.80371.5326-0.17680.3272-0.171-0.42840.0138-0.3890.1440.1150.1630.40970.05140.20180.4435-0.06680.168720.244-52.606-44.323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 397
2X-RAY DIFFRACTION2B3 - 397
3X-RAY DIFFRACTION3C3 - 397
4X-RAY DIFFRACTION4D3 - 397

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