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- PDB-5t8t: Crystal Structure of a S-adenosylmethionine Synthase from Neisser... -

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Basic information

Entry
Database: PDB / ID: 5t8t
TitleCrystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound AMP 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
ADENOSINE MONOPHOSPHATE / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 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 AMP 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 5, 2016Group: Data collection
Revision 1.2Oct 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_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)86,4074
Polymers86,0352
Non-polymers3722
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-31 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.580, 116.580, 145.600
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-524-

HOH

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Components

#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
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NegoA.00040.a.B1.PW37902 at 20.8 mg/ml, mixed 1:1 with an equal volume Morpheus(b9): 10% (w/v) PEG-20000, 20% (v/v) PEG MME 550, 0.1 M bicine/Trizma base, pH = 8.5, 0.03 M each NaF, NaBr, NaI

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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: 2.1→50 Å / Num. obs: 58908 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 28.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
2.1-2.157.30.5773.140.911100
2.15-2.210.4873.780.93599.9
2.21-2.280.4024.670.95499.9
2.28-2.350.3545.430.96399.9
2.35-2.420.36.380.974100
2.42-2.510.2667.180.977100
2.51-2.60.2178.390.98499.9
2.6-2.710.1869.590.98899.9
2.71-2.830.15910.830.99100
2.83-2.970.13212.750.99399.8
2.97-3.130.11514.510.99499.8
3.13-3.320.09916.380.99599.8
3.32-3.550.0918.420.99599.5
3.55-3.830.08320.130.99599.5
3.83-4.20.07821.70.99599.3
4.2-4.70.07422.610.99599
4.7-5.420.06722.880.99698.9
5.42-6.640.06122.520.99798.3
6.64-9.390.0523.530.99897.5
9.390.04822.220.99793.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2499: ???refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5T8S

5t8s


Resolution: 2.1→45.502 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.56
RfactorNum. reflection% reflection
Rfree0.2055 2067 3.51 %
Rwork0.1702 --
obs0.1715 58889 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.09 Å2 / Biso mean: 37.8522 Å2 / Biso min: 13.54 Å2
Refinement stepCycle: final / Resolution: 2.1→45.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5621 0 24 382 6027
Biso mean--43.9 40.9 -
Num. residues----754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075813
X-RAY DIFFRACTIONf_angle_d0.87927
X-RAY DIFFRACTIONf_chiral_restr0.052913
X-RAY DIFFRACTIONf_plane_restr0.0061037
X-RAY DIFFRACTIONf_dihedral_angle_d15.8023505
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.24051350.218137513886100
2.1489-2.20260.2911420.208537503892100
2.2026-2.26220.23821120.193537533865100
2.2622-2.32870.20511480.190837313879100
2.3287-2.40390.21221460.175837263872100
2.4039-2.48980.23431400.173237643904100
2.4898-2.58950.21341320.171437693901100
2.5895-2.70730.22291360.171237653901100
2.7073-2.850.21571240.17537923916100
2.85-3.02860.19521310.182837703901100
3.0286-3.26230.21351300.181938103940100
3.2623-3.59050.19971320.174338153947100
3.5905-4.10980.17981540.14823799395399
4.1098-5.17670.1781500.14073854400499
5.1767-45.51230.21211550.17373973412897
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)
11.3485-0.0852-0.34032.0512-0.81543.12060.00190.03-0.0729-0.0293-0.0438-0.00030.35750.10270.04660.1571-0.00930.01010.23310.00730.221837.7784-23.91438.5829
21.70880.92780.14221.50330.41631.45440.00230.12230.2268-0.10250.06860.0732-0.10340.0782-0.07820.15070.02390.05740.26330.04690.270345.2907-5.9878-2.4666
31.29770.2288-0.39871.63990.26472.4334-0.10960.2705-0.1219-0.30650.1166-0.2360.33050.42350.02240.26580.03340.06320.3515-0.0250.247744.0887-26.5786-13.2932
41.5879-0.2432-0.62451.4945-0.07952.10510.02550.21280.0648-0.0234-0.00480.0725-0.1105-0.1374-0.05850.1306-0.0623-0.01270.17790.02320.176418.9311-17.83820.8988
56.38422.7053-0.24035.33653.94847.3003-0.06020.0533-0.57150.3577-0.03180.19230.8439-0.26310.06460.2539-0.0722-0.00950.21810.02380.236711.3176-28.41797.7334
60.776-0.0859-0.37751.3885-0.50932.24580.02620.3070.1903-0.2150.0292-0.0343-0.268-0.0692-0.03350.220.0055-0.01820.28920.02230.246119.1918-15.9448-8.9251
72.25340.49480.15182.12780.87012.0009-0.08020.3681-0.3153-0.17570.09290.00850.42560.0780.00220.3382-0.0612-0.0070.2824-0.06710.268818.4912-36.2512-14.8382
80.9805-0.8551-0.1852.1404-0.33363.29920.16720.30560.373-0.441-0.0069-0.1282-0.4466-0.1807-0.11820.3247-0.01880.04220.34270.0880.32420.8089-6.2383-15.0768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 104 )A2 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 244 )A114 - 244
3X-RAY DIFFRACTION3chain 'A' and (resid 245 through 389 )A245 - 389
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 64 )B2 - 64
5X-RAY DIFFRACTION5chain 'B' and (resid 65 through 90 )B65 - 90
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 156 )B91 - 156
7X-RAY DIFFRACTION7chain 'B' and (resid 157 through 247 )B157 - 247
8X-RAY DIFFRACTION8chain 'B' and (resid 248 through 388 )B248 - 388

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