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- PDB-6sw6: Crystal structure R264H mutant of the human S-adenosylmethionine ... -

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Basic information

Entry
Database: PDB / ID: 6sw6
TitleCrystal structure R264H mutant of the human S-adenosylmethionine synthetase 1
ComponentsS-adenosylmethionine synthase isoform type-1
KeywordsTRANSFERASE / S-adenosylmethionine synthesis
Function / homology
Function and homology information


Defective MAT1A causes MATD / methionine catabolic process / Sulfur amino acid metabolism / methionine adenosyltransferase complex / Metabolism of ingested SeMet, Sec, MeSec into H2Se / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / one-carbon metabolic process ...Defective MAT1A causes MATD / methionine catabolic process / Sulfur amino acid metabolism / methionine adenosyltransferase complex / Metabolism of ingested SeMet, Sec, MeSec into H2Se / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / one-carbon metabolic process / protein homotetramerization / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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.
Similarity search - Domain/homology
S-adenosylmethionine synthase isoform type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPanmanee, J. / Antonyuk, S.V. / Hasnain, S.S.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structural basis of the dominant inheritance of hypermethioninemia associated with the Arg264His mutation in the MAT1A gene.
Authors: Panmanee, J. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionSep 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine synthase isoform type-1
B: S-adenosylmethionine synthase isoform type-1


Theoretical massNumber of molelcules
Total (without water)87,3702
Polymers87,3702
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-28 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.558, 83.619, 87.562
Angle α, β, γ (deg.)90.000, 107.990, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 16 - 395 / Label seq-ID: 16 - 395

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein S-adenosylmethionine synthase isoform type-1 / AdoMet synthase 1 / Methionine adenosyltransferase 1 / MAT 1 / Methionine adenosyltransferase I/III ...AdoMet synthase 1 / Methionine adenosyltransferase 1 / MAT 1 / Methionine adenosyltransferase I/III / MAT-I/III


Mass: 43684.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Liver / Cell: Hepatocyte / Gene: MAT1A, AMS1, MATA1 / Organ: Liver / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00266, methionine adenosyltransferase
#2: Water ChemComp-HOH / water / 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: 2.3 Å3/Da / Density % sol: 46.62 % / Description: Pyramidal crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 200 mM NaF, 20 % PEG 3350 and 15 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.85→51.87 Å / Num. obs: 17484 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 55.573 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.092 / Rrim(I) all: 0.211 / Net I/σ(I): 5.1
Reflection shellResolution: 2.85→3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2499 / CC1/2: 0.755 / Rpim(I) all: 0.447 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OBV

2obv


Resolution: 2.85→51.87 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.865 / SU B: 23.967 / SU ML: 0.451 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.491
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 882 5.1 %RANDOM
Rwork0.2607 ---
obs0.262 16552 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.14 Å2 / Biso mean: 59.422 Å2 / Biso min: 31.44 Å2
Baniso -1Baniso -2Baniso -3
1--4.14 Å20 Å2-4.34 Å2
2--4.95 Å20 Å2
3---1.66 Å2
Refinement stepCycle: final / Resolution: 2.85→51.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5693 0 0 4 5697
Biso mean---34.44 -
Num. residues----739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195803
X-RAY DIFFRACTIONr_bond_other_d0.0020.025374
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9557859
X-RAY DIFFRACTIONr_angle_other_deg0.897312438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8855734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5523.969257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71215979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7831538
X-RAY DIFFRACTIONr_chiral_restr0.0640.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021169
Refine LS restraints NCS

Ens-ID: 1 / Number: 22022 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 57 -
Rwork0.333 1193 -
all-1250 -
obs--99.76 %

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