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- PDB-4ws9: Crystal structure of sMAT N159G from Sulfolobus solfataricus -

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Basic information

Entry
Database: PDB / ID: 4ws9
TitleCrystal structure of sMAT N159G from Sulfolobus solfataricus
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / S-adenosylmethionine
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding
Similarity search - Function
S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, archaea / S-adenosylmethionine synthase / S-adenosylmethionine synthetase, domain 3 / S-adenosylmethionine synthetase (AdoMet synthetase) / GMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsWang, F. / Brady, E.L. / Singh, S. / Clinger, J.A. / Huber, T.D. / Thorson, J.S. / Phillips Jr., G.N.
CitationJournal: To Be Published
Title: Crystal structure of sMAT N159G from Sulfolobus solfataricus.
Authors: Brady, E.L. / Wang, F. / Singh, S. / Clinger, J.A. / Huber, T.D. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionOct 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _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
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
E: S-adenosylmethionine synthase
F: S-adenosylmethionine synthase
G: S-adenosylmethionine synthase
H: S-adenosylmethionine synthase
I: S-adenosylmethionine synthase
J: S-adenosylmethionine synthase
K: S-adenosylmethionine synthase
L: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)550,01630
Polymers548,30712
Non-polymers1,70918
Water16,970942
1
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,33910
Polymers182,7694
Non-polymers5706
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15890 Å2
ΔGint-102 kcal/mol
Surface area56120 Å2
MethodPISA
2
E: S-adenosylmethionine synthase
F: S-adenosylmethionine synthase
G: S-adenosylmethionine synthase
H: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,33910
Polymers182,7694
Non-polymers5706
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15890 Å2
ΔGint-105 kcal/mol
Surface area55910 Å2
MethodPISA
3
I: S-adenosylmethionine synthase
J: S-adenosylmethionine synthase
K: S-adenosylmethionine synthase
L: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,33910
Polymers182,7694
Non-polymers5706
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15900 Å2
ΔGint-105 kcal/mol
Surface area56190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.716, 289.202, 174.686
Angle α, β, γ (deg.)90.000, 99.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H
91chain I
101chain J
111chain K
121chain L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: PHE / End label comp-ID: PHE

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ILEILEchain AAA0 - 4049 - 413
2ARGARGchain BBB2 - 40411 - 413
3ILEILEchain CCC0 - 4049 - 413
4ARGARGchain DDD2 - 40411 - 413
5ILEILEchain EEE0 - 4049 - 413
6ARGARGchain FFF2 - 40411 - 413
7ILEILEchain GGG0 - 4049 - 413
8ARGARGchain HHH2 - 40411 - 413
9ILEILEchain III0 - 4049 - 413
10ARGARGchain JJJ2 - 40411 - 413
11ILEILEchain KKK0 - 4049 - 413
12ARGARGchain LLL2 - 40411 - 413

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Components

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


Mass: 45692.238 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: mat, SSO0199 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q980S9, methionine adenosyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 942 / 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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.1M-1.6M LiSO4, 0.1M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 134821 / % possible obs: 75.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.079 / Rrim(I) all: 0.16 / Rsym value: 0.16 / Χ2: 0.512 / Net I/av σ(I): 5.105 / Net I/σ(I): 4.4 / Num. measured all: 527284
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.8-2.853.90.87950050.6060.4760.56756.3
2.85-2.940.7550810.6840.4040.5657.50.856
2.9-2.964.10.70851840.7160.3810.57458.50.807
2.96-3.024.10.63153150.7630.3410.578600.721
3.02-3.084.10.55554210.7910.3010.5961.30.633
3.08-3.1540.48256030.8290.2620.59863.20.551
3.15-3.2340.45657370.8590.2480.59464.40.521
3.23-3.3240.37658590.8760.2050.59566.50.43
3.32-3.4240.27860170.9340.1530.59967.40.319
3.42-3.533.90.23761570.9450.1310.60269.80.272
3.53-3.653.90.18764500.9660.1040.56272.90.215
3.65-3.83.80.16767460.9730.0930.54975.90.192
3.8-3.973.70.13771980.9780.0770.503810.158
3.97-4.183.60.11475990.9860.0650.48685.60.132
4.18-4.443.70.09779900.9910.0550.4490.10.112
4.44-4.783.70.08682690.9940.0480.44293.50.099
4.78-5.263.80.09185850.9930.0510.44596.30.105
5.26-6.023.90.10287380.990.0560.42798.40.117
6.02-7.564.10.08789090.9930.0480.41699.70.1
7.56-304.20.04589580.990.0250.38299.70.052

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIX1.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K0B

4k0b


Resolution: 2.803→30 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 1527 1.13 %Random selection
Rwork0.2209 133058 --
obs0.2213 134585 75.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 380.2 Å2 / Biso mean: 53.4169 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 2.803→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36534 0 90 942 37566
Biso mean--129.58 44.04 -
Num. residues----4698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01637122
X-RAY DIFFRACTIONf_angle_d1.61550226
X-RAY DIFFRACTIONf_chiral_restr0.085898
X-RAY DIFFRACTIONf_plane_restr0.0096462
X-RAY DIFFRACTIONf_dihedral_angle_d12.88313998
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A22907X-RAY DIFFRACTION9.057TORSIONAL
12B22907X-RAY DIFFRACTION9.057TORSIONAL
13C22907X-RAY DIFFRACTION9.057TORSIONAL
14D22907X-RAY DIFFRACTION9.057TORSIONAL
15E22907X-RAY DIFFRACTION9.057TORSIONAL
16F22907X-RAY DIFFRACTION9.057TORSIONAL
17G22907X-RAY DIFFRACTION9.057TORSIONAL
18H22907X-RAY DIFFRACTION9.057TORSIONAL
19I22907X-RAY DIFFRACTION9.057TORSIONAL
110J22907X-RAY DIFFRACTION9.057TORSIONAL
111K22907X-RAY DIFFRACTION9.057TORSIONAL
112L22907X-RAY DIFFRACTION9.057TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8035-2.89390.378990.32818589868854
2.8939-2.99720.32471110.31369390950159
2.9972-3.11710.36851100.30669835994562
3.1171-3.25880.32561350.3085102621039765
3.2588-3.43040.31381210.2745107571087867
3.4304-3.6450.27661260.2498113611148771
3.645-3.92590.24521490.2373124501259978
3.9259-4.31990.26941510.2018137911394287
4.3199-4.94260.21111470.1722149431509093
4.9426-6.2180.23621810.1974157021588398
6.218-30.01680.1991970.1744159781617599
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)
10.56880.6057-0.69933.028-0.23063.4005-0.0640.09180.0636-0.21130.04540.1651-0.042-0.11620.02310.14330.0589-0.03670.3112-0.01240.4121-74.0968-52.41214.4219
20.62120.4094-0.11962.56240.02953.1738-0.0256-0.0039-0.0941-0.2081-0.0697-0.43840.27420.48230.04640.19190.18450.04410.43760.07650.4964-50.0593-56.084118.9902
30.3344-0.151-0.18452.1355-0.32963.5554-0.0024-0.1213-0.00340.5556-0.0227-0.16530.13360.32290.02980.60020.072-0.03580.42030.07830.4031-58.0022-54.498268.9728
40.4918-0.3853-0.14452.47040.22343.1515-0.0009-0.14520.00980.3864-0.0750.42050.2112-0.41550.03670.4577-0.08140.10120.4253-0.03970.5053-82.3261-54.5264.3145
50.41030.1236-0.01233.1307-0.13493.70170.00260.02620.0462-0.3133-0.0021-0.0732-0.22140.19840.00390.00580.0416-0.02110.3237-0.03550.3552-82.5485-101.6391-11.6677
60.63960.2305-0.09462.5132-0.09552.12280.09620.02360.1232-0.1814-0.11340.4378-0.3434-0.5509-0.03440.0620.1729-0.0240.4925-0.06130.5072-107.1542-103.3892-13.7045
70.72550.0249-0.43663.93210.00472.57450.0024-0.0185-0.04870.6868-0.10270.40350.5643-0.33860.09820.3228-0.13530.1260.4683-0.0690.4058-107.3648-147.784110.4216
81.0890.0829-0.43392.9525-0.12892.18470.0178-0.1604-0.07130.81830.0104-0.37720.44420.24530.02850.7709-0.0287-0.16310.289-0.00840.3106-83.4031-144.342715.5193
90.63330.0832-0.47373.27330.13672.6701-0.06340.1085-0.0764-0.3217-0.0427-0.28070.17230.42910.120.7118-0.01960.09020.55030.04790.3883-96.5487-146.482976.7841
101.0219-0.232-0.38772.16410.10412.3487-0.01580.2028-0.1048-0.76950.07380.31060.375-0.26230.08020.9873-0.0614-0.10790.4312-0.04070.3112-120.8403-146.101371.9907
110.7303-0.25250.15032.39910.49892.9981-0.16830.02660.1563-0.25820.08130.1736-0.6674-0.18440.01680.74260.0131-0.11570.35930.08130.3633-126.5631-103.096898.2664
121.0296-0.21580.10882.21770.43292.1875-0.03320.03020.2379-0.35720.0716-0.2824-0.7540.53360.0720.8122-0.27380.03090.44220.05770.4061-101.9057-101.8834100.0187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 404)A0
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 500)B0
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 404)C0
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 404)D0
5X-RAY DIFFRACTION5(chain 'E' and resid 0 through 404)E0
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 500)F0
7X-RAY DIFFRACTION7(chain 'G' and resid 0 through 404)G0
8X-RAY DIFFRACTION8(chain 'H' and resid 2 through 404)H0
9X-RAY DIFFRACTION9(chain 'I' and resid 0 through 404)I0
10X-RAY DIFFRACTION10(chain 'J' and resid 2 through 500)J0
11X-RAY DIFFRACTION11(chain 'K' and resid 0 through 404)K0
12X-RAY DIFFRACTION12(chain 'L' and resid 2 through 404)L0

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