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- PDB-5t8s: Crystal Structure of a S-adenosylmethionine Synthase from Neisser... -

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Basic information

Entry
Database: PDB / ID: 5t8s
TitleCrystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / SSGCID / S-adenosylmethionine synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding / cytoplasm
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
TRIPHOSPHATE / ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / PYROPHOSPHATE 2- / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium
Authors: Dranow, D.M. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,40711
Polymers86,0352
Non-polymers1,3729
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-70 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.710, 115.710, 146.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21A-824-

HOH

31A-852-

HOH

41B-809-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 43017.488 Da / Num. of mol.: 2 / Fragment: NegoA.00040.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: metK, NGO0106 / Plasmid: NegoA.00040.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5FAC0, methionine adenosyltransferase

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Non-polymers , 7 types, 697 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#7: Chemical ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NegoA.00040.a.B1.PW37902 at 20.8 mg/ml, mixed with 2 mM each ATP, 2 mM L-Met, and 2 mM MgCl2, then mixed 1:1 and incubated with an equal volume Morpheus(f12): 12.5% (w/v) PEG-1000, 12.5 % ...Details: NegoA.00040.a.B1.PW37902 at 20.8 mg/ml, mixed with 2 mM each ATP, 2 mM L-Met, and 2 mM MgCl2, then mixed 1:1 and incubated with an equal volume Morpheus(f12): 12.5% (w/v) PEG-1000, 12.5 % (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M bicine/Trizma base, pH = 8.5, 0.02 M each D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 108870 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 16.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
1.7-1.7412.40.5684.960.93699.5
1.74-1.790.4855.730.95199.6
1.79-1.840.387.240.97199.6
1.84-1.90.3058.880.97999.5
1.9-1.960.2510.630.98599.7
1.96-2.030.19213.390.99199.6
2.03-2.110.1615.770.99399.8
2.11-2.190.13118.780.99599.7
2.19-2.290.1121.650.99699.8
2.29-2.40.09624.060.99799.9
2.4-2.530.08726.420.99799.9
2.53-2.690.07629.410.99899.9
2.69-2.870.06932.480.998100
2.87-3.10.0636.870.998100
3.1-3.40.05440.680.999100
3.4-3.80.0543.870.999100
3.8-4.390.04846.280.998100
4.39-5.380.04647.240.999100
5.38-7.60.04745.710.999100
7.60.04744.080.99898.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2499: ???refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IML

3iml


Resolution: 1.7→37.278 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.18
RfactorNum. reflection% reflection
Rfree0.1706 1954 1.83 %
Rwork0.1484 --
obs0.1488 106709 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.04 Å2 / Biso mean: 24.684 Å2 / Biso min: 7.35 Å2
Refinement stepCycle: final / Resolution: 1.7→37.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5715 0 81 691 6487
Biso mean--17.15 34.92 -
Num. residues----764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066080
X-RAY DIFFRACTIONf_angle_d0.8748323
X-RAY DIFFRACTIONf_chiral_restr0.057950
X-RAY DIFFRACTIONf_plane_restr0.0061089
X-RAY DIFFRACTIONf_dihedral_angle_d14.5363687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74260.2091320.1757005713793
1.7426-1.78970.18221320.17467098723094
1.7897-1.84230.24421340.16577203733795
1.8423-1.90180.18651390.15967307744697
1.9018-1.96980.19331370.16087344748197
1.9698-2.04860.17991350.14997415755098
2.0486-2.14190.18091390.15137491763098
2.1419-2.25480.19311370.14527498763599
2.2548-2.3960.16341430.14847569771299
2.396-2.5810.16741420.148576177759100
2.581-2.84060.15941430.150676487791100
2.8406-3.25150.16751440.151476967840100
3.2515-4.09570.15671460.135577937939100
4.0957-37.28740.15631510.14218071822299
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)
10.88920.41090.29220.63840.15120.694-0.0070.05870.0508-0.04410.00760.0661-0.0839-0.0342-0.02530.0764-0.0025-0.00760.09210.01010.109418.302181.210276.4391
21.90580.49370.41371.31420.45211.23480.09950.2145-0.3626-0.03060.0575-0.07380.16890.0934-0.10220.11760.0159-0.05750.1214-0.03860.206911.962456.880472.1296
31.06160.30070.44070.94420.03631.3131-0.08220.22250.0307-0.17760.08250.0733-0.06-0.0484-0.00550.1169-0.0434-0.02370.16390.01720.118518.915481.204361.8905
40.90710.12030.5911.18740.16251.488-0.11670.2390.1899-0.23770.05980.2784-0.2197-0.25950.070.1598-0.0044-0.06750.24720.04630.20058.952587.211360.1397
51.34410.44520.71320.95020.73151.66950.01030.167-0.07530.10160.0827-0.08940.03060.2249-0.08090.0784-0.02750.01130.1375-0.0220.116541.381978.609176.2504
60.79840.28620.46750.88880.36550.9036-0.00220.3494-0.1768-0.13370.0882-0.04970.14170.2279-0.01860.14410.00390.0190.2602-0.03910.184438.699173.868765.066
70.455-0.3453-0.14360.9915-0.54690.5329-0.17110.44880.1152-0.14370.104-0.0414-0.15960.2526-0.06480.1819-0.14390.0070.32120.03770.12941.272491.127859.3084
81.1143-0.2322-0.56660.413-0.24980.7405-0.26080.49730.355-0.24720.0530.0549-0.44650.0725-0.14540.2661-0.1775-0.01570.34970.10320.167439.503695.853455.7479
90.9859-0.080.24241.30330.22121.40180.05240.3664-0.2556-0.22020.10120.00330.20690.172-0.13630.1773-0.0175-0.0170.2676-0.06470.197332.190267.668761.0674
100.09290.14460.16031.1740.31032.06260.13140.5031-0.4774-0.29720.0921-0.2220.46330.5678-0.15920.30470.0804-0.02570.4551-0.19610.366941.167561.609658.3249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 156 )A2 - 156
2X-RAY DIFFRACTION2chain 'A' and (resid 157 through 238 )A157 - 238
3X-RAY DIFFRACTION3chain 'A' and (resid 239 through 326 )A239 - 326
4X-RAY DIFFRACTION4chain 'A' and (resid 327 through 389 )A327 - 389
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 90 )B2 - 90
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 156 )B91 - 156
7X-RAY DIFFRACTION7chain 'B' and (resid 157 through 176 )B157 - 176
8X-RAY DIFFRACTION8chain 'B' and (resid 177 through 238 )B177 - 238
9X-RAY DIFFRACTION9chain 'B' and (resid 239 through 326 )B239 - 326
10X-RAY DIFFRACTION10chain 'B' and (resid 327 through 389 )B327 - 389

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