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- PDB-5a19: The structure of MAT2A in complex with PPNP. -

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Basic information

Entry
Database: PDB / ID: 5a19
TitleThe structure of MAT2A in complex with PPNP.
ComponentsS-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2
KeywordsTRANSFERASE / METHIONINE ADENOSYLTRANSFERASE / CELL GROWTH / LIVER CANCER / METHYLATION.
Function / homology
Function and homology information


methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process / ATP binding / identical protein 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
: / DI(HYDROXYETHYL)ETHER / (DIPHOSPHONO)AMINOPHOSPHONIC ACID / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsMurray, B. / Antonyuk, S.V. / Marina, A. / Lu, S.C. / Mato, J.M. / Hasnain, S.S. / Rojas, A.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Crystallography Captures Catalytic Steps in Human Methionine Adenosyltransferase Enzymes.
Authors: Murray, B. / Antonyuk, S.V. / Marina, A. / Lu, S.C. / Mato, J.M. / Hasnain, S.S. / Rojas, A.L.
History
DepositionApr 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,72210
Polymers43,7211
Non-polymers1,0019
Water2,612145
1
A: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2
hetero molecules

A: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,44420
Polymers87,4412
Non-polymers2,00218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7790 Å2
ΔGint-29.2 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.220, 95.490, 117.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2104-

HOH

21A-2144-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2 / ADOMET SYNTHASE 2 / METHIONINE ADENOSYLTRANSFERASE 2 / MAT MAT2 / METHIONINE ADENOSYLTRANSFERASE II ...ADOMET SYNTHASE 2 / METHIONINE ADENOSYLTRANSFERASE 2 / MAT MAT2 / METHIONINE ADENOSYLTRANSFERASE II / MAT-II / METHIONINE ADENOSYLTRANSFERASE 2A


Mass: 43720.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P31153, methionine adenosyltransferase

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Non-polymers , 7 types, 154 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID


Mass: 256.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H6NO9P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 39 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 30 % PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 11, 2014 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.33→74.04 Å / Num. obs: 16225 / % possible obs: 99.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 20.7
Reflection shellResolution: 2.34→2.4 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P02

2p02


Resolution: 2.34→57.71 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.69 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20446 805 5 %RANDOM
Rwork0.16344 ---
obs0.16549 15301 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.141 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.34→57.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 60 145 3073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192976
X-RAY DIFFRACTIONr_bond_other_d0.0020.022882
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9784010
X-RAY DIFFRACTIONr_angle_other_deg0.88536643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6223.906128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2481519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213298
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02647
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_it1.042.7181474
X-RAY DIFFRACTIONr_mcbond_other1.0382.7181473
X-RAY DIFFRACTIONr_mcangle_it1.7264.0711839
X-RAY DIFFRACTIONr_mcangle_other1.7254.0731840
X-RAY DIFFRACTIONr_scbond_it1.0352.9071502
X-RAY DIFFRACTIONr_scbond_other1.0352.9071502
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6744.2812172
X-RAY DIFFRACTIONr_long_range_B_refined3.59121.5113235
X-RAY DIFFRACTIONr_long_range_B_other3.34921.3753189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 62 -
Rwork0.179 1111 -
obs--99.83 %

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