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- PDB-4hpv: Crystal structure of S-Adenosylmethionine synthetase from Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 4hpv
TitleCrystal structure of S-Adenosylmethionine synthetase from Sulfolobus solfataricus
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
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
S-adenosylmethionine synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.214 Å
AuthorsWang, F. / Hurley, K.A. / Helmich, K.E. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Febs J. / Year: 2014
Title: Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT from Sulfolobus solfataricus.
Authors: Wang, F. / Singh, S. / Zhang, J. / Huber, T.D. / Helmich, K.E. / Sunkara, M. / Hurley, K.A. / Goff, R.D. / Bingman, C.A. / Morris, A.J. / Thorson, J.S. / Phillips, G.N.
History
DepositionOct 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references / Source and taxonomy / Structure summary
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Oct 8, 2014Group: Database references
Revision 1.4Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn_radiation_wavelength / software / Item: _diffrn_radiation_wavelength.wavelength

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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


Theoretical massNumber of molelcules
Total (without water)90,6612
Polymers90,6612
Non-polymers00
Water5,477304
1
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase

A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase


Theoretical massNumber of molelcules
Total (without water)181,3234
Polymers181,3234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area13410 Å2
ΔGint-57 kcal/mol
Surface area57790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.304, 151.304, 221.145
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-576-

HOH

21B-602-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -y+1,-x+1,-z+1/6

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Components

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


Mass: 45330.684 Da / Num. of mol.: 2
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, Ssol_1180 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980S9, methionine adenosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Protein Solution (6.8-13.5 mg/ml protein, 25mM Tris pH 8.0) mixed in a 1:1 ratio with the well solution (1.4M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 5.6) ...Details: Protein Solution (6.8-13.5 mg/ml protein, 25mM Tris pH 8.0) mixed in a 1:1 ratio with the well solution (1.4M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 5.6) Cryoprotected with 20% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.97856
SYNCHROTRONAPS 21-ID-G20.97856
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDFeb 11, 2012
MARMOSAIC 300 mm CCD2CCDMar 8, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond [111]SINGLE WAVELENGTHMx-ray1
2Diamond [111]SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
20.978561
ReflectionResolution: 2.21→50 Å / Num. all: 75422 / Num. obs: 74442 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.9 % / Biso Wilson estimate: 42.94 Å2 / Rmerge(I) obs: 0.118 / Χ2: 0.873 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible all
2.21-2.259.228300.696176.6
2.25-2.2912.136530.666198.5
2.29-2.3314.636790.684199.4
2.33-2.3817.736850.691100
2.38-2.4319.437220.7031100
2.43-2.4920.137220.7121100
2.49-2.5520.437120.7221100
2.55-2.6220.637300.7561100
2.62-2.72137090.771100
2.7-2.7821.237330.8071100
2.78-2.8821.537520.8521100
2.88-321.837310.9051100
3-3.1422.137601.0061100
3.14-3.322.237731.0741100
3.3-3.5122.337721.081100
3.51-3.7822.237991.0561100
3.78-4.1622.137921.0751100
4.16-4.7621.938511.051100
4.76-621.638981.081100
6-5020.141390.6541100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXPHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.214→49.526 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.8324 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 3730 5.02 %RAMDOM, ASSIGN TEST SET IN THIN RESOLUTION SHELLS
Rwork0.199 ---
obs0.2 74289 99.51 %-
all-74655 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.22 Å2 / Biso mean: 38.372 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: LAST / Resolution: 2.214→49.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6192 0 0 304 6496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026403
X-RAY DIFFRACTIONf_angle_d0.6858677
X-RAY DIFFRACTIONf_chiral_restr0.0481013
X-RAY DIFFRACTIONf_plane_restr0.0021127
X-RAY DIFFRACTIONf_dihedral_angle_d11.7252438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2142-2.24220.36981800.30972274245491
2.2422-2.27170.2835268098
2.2717-2.30290.31061840.26982506269099
2.3029-2.33580.28521870.265125042691100
2.3358-2.37060.2881870.250525432730100
2.3706-2.40770.23872722100
2.4077-2.44710.28311870.234125432730100
2.4471-2.48930.26781870.228625172704100
2.4893-2.53460.30071870.224425422729100
2.5346-2.58330.22092736100
2.5833-2.63610.26351870.2225492736100
2.6361-2.69340.24831870.214825282715100
2.6934-2.7560.2518540.210227012755100
2.756-2.8250.27111330.217125992732100
2.825-2.90130.25041870.20825732760100
2.9013-2.98670.21451870.213425602747100
2.9867-3.08310.20932751100
3.0831-3.19320.24521870.207725662753100
3.1932-3.32110.24031870.198925672754100
3.3211-3.47220.23021870.193425822769100
3.4722-3.65520.18172778100
3.6552-3.88410.19671870.181326052792100
3.8841-4.18390.18241870.164326112798100
4.1839-4.60460.17541870.160126272814100
4.6046-5.27030.15962846100
5.2703-6.63750.1861870.219826842871100
6.6375-49.53820.19421870.20982865305299

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