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- PDB-6fwb: Crystal structure of Mat2A at 1.79 Angstron resolution -

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Basic information

Entry
Database: PDB / ID: 6fwb
TitleCrystal structure of Mat2A at 1.79 Angstron resolution
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsHYDROLASE / S-adenosylmethionine synthetase 2
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
S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsZhou, A. / Wei, Z. / Bai, J. / Wang, H.
CitationJournal: Ebiomedicine / Year: 2019
Title: Identification of a natural inhibitor of methionine adenosyltransferase 2A regulating one-carbon metabolism in keratinocytes.
Authors: Bai, J. / Gao, Y. / Chen, L. / Yin, Q. / Lou, F. / Wang, Z. / Xu, Z. / Zhou, H. / Li, Q. / Cai, W. / Sun, Y. / Niu, L. / Wang, H. / Wei, Z. / Lu, S. / Zhou, A. / Zhang, J. / Wang, H.
History
DepositionMar 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
B: S-adenosylmethionine synthase isoform type-2
A: S-adenosylmethionine synthase isoform type-2
C: S-adenosylmethionine synthase isoform type-2
D: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,50233
Polymers182,1104
Non-polymers3,39229
Water9,386521
1
B: S-adenosylmethionine synthase isoform type-2
A: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,38823
Polymers91,0552
Non-polymers2,33321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-240 kcal/mol
Surface area26950 Å2
MethodPISA
2
C: S-adenosylmethionine synthase isoform type-2
D: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,11410
Polymers91,0552
Non-polymers1,0598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-79 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.430, 103.027, 114.465
Angle α, β, γ (deg.)90.00, 93.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14A
24C
15A
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUBA16 - 39332 - 409
21GLYGLYLEULEUAB16 - 39332 - 409
12GLUGLULEULEUBA15 - 39331 - 409
22GLUGLULEULEUCC15 - 39331 - 409
13GLUGLULYSLYSBA15 - 39431 - 410
23GLUGLULYSLYSDD15 - 39431 - 410
14GLYGLYLEULEUAB16 - 39332 - 409
24GLYGLYLEULEUCC16 - 39332 - 409
15GLYGLYLYSLYSAB16 - 39432 - 410
25GLYGLYLYSLYSDD16 - 39432 - 410
16GLUGLULEULEUCC15 - 39331 - 409
26GLUGLULEULEUDD15 - 39331 - 409

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules BACD

#1: Protein
S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II


Mass: 45527.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P31153, methionine adenosyltransferase

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Non-polymers , 5 types, 550 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.4 / Details: 35% PEG 1000, 0.1M Hepes, 50mM Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.07822 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07822 Å / Relative weight: 1
ReflectionResolution: 1.79→57.13 Å / Num. obs: 147112 / % possible obs: 98.8 % / Redundancy: 7.1 % / Net I/σ(I): 12.7
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10821 / CC1/2: 0.737 / Rpim(I) all: 0.365 / Rrim(I) all: 0.961 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→57.13 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.566 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18317 7197 4.9 %RANDOM
Rwork0.17186 ---
obs0.17244 139387 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.842 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.39 Å2
2---0.52 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.79→57.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11425 0 199 521 12145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911877
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211192
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.97616051
X-RAY DIFFRACTIONr_angle_other_deg0.964325969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26351482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52923.957513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.057152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2351577
X-RAY DIFFRACTIONr_chiral_restr0.0940.21793
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113060
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022333
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_it1.0482.185910
X-RAY DIFFRACTIONr_mcbond_other1.0482.185909
X-RAY DIFFRACTIONr_mcangle_it1.6993.2597383
X-RAY DIFFRACTIONr_mcangle_other1.6993.267384
X-RAY DIFFRACTIONr_scbond_it1.4432.4915967
X-RAY DIFFRACTIONr_scbond_other1.4412.4915967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.273.6338664
X-RAY DIFFRACTIONr_long_range_B_refined5.22825.82512633
X-RAY DIFFRACTIONr_long_range_B_other5.22825.83112634
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B231460.11
12A231460.11
21B238860.07
22C238860.07
31B230740.11
32D230740.11
41A228460.1
42C228460.1
51A239380.07
52D239380.07
61C229220.1
62D229220.1
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 465 -
Rwork0.271 10229 -
obs--97.5 %
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)
10.5784-0.06730.23770.573-0.11080.4954-0.0044-0.0671-0.07280.0492-0.00770.08180.0705-0.07520.0120.02960.00280.02160.03620.00430.07181.9733-20.8751169.891
20.7447-0.01390.05120.4658-0.00160.5569-0.0417-0.08150.08550.0592-0.00190.018-0.1141-0.01530.04360.03810.0155-0.02140.0246-0.02370.051611.73151.4567171.5092
30.5095-0.20470.35161.0763-0.57632.25990.04790.1669-0.0222-0.3451-0.2661-0.1710.24950.53360.21820.13610.11280.06810.17240.05810.051719.5973-7.6081117.1301
40.6240.1324-0.14740.5335-0.39331.1509-0.01720.1403-0.0635-0.1794-0.05910.04750.0349-0.15390.07630.12170.0522-0.05120.0871-0.04950.0352-3.8539-0.4967117.9122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B13 - 394
2X-RAY DIFFRACTION2A16 - 394
3X-RAY DIFFRACTION3C15 - 393
4X-RAY DIFFRACTION4D15 - 394

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