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- PDB-8ws2: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 8ws2
TitleCrystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTRANSFERASE / MTAP / complex / phosphorylase
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsIizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine
Authors: Iizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.
History
DepositionOct 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5326
Polymers30,7771
Non-polymers7555
Water2,702150
1
A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules

A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules

A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,59618
Polymers92,3323
Non-polymers2,26415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12430 Å2
ΔGint-63 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.646, 77.646, 230.39
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

21A-625-

HOH

31A-647-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein S-methyl-5'-thioadenosine phosphorylase / 5'-methylthioadenosine phosphorylase / MTA phosphorylase / MTAP


Mass: 30777.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first M and second F are missing in the uploaded structure because the electron density could not be observed.
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Gene: mtnP, APE_1885 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9YAQ8, S-methyl-5'-thioadenosine phosphorylase

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Non-polymers , 5 types, 155 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 293.2 K / Method: counter-diffusion / pH: 5.4
Details: The mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir ...Details: The mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows.15%(v/v)PEG#200,0.1 M phosphate citrate pH 5.4, 5 mM MTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→43.74 Å / Num. obs: 79813 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.053 / Rrim(I) all: 0.12 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.22-1.24102.22138950.3821.0922.48
6.68-43.7490.02350460.9990.0110.025

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
Coot0.9.8.95model building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WTA

1wta


Resolution: 1.22→38.853 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.585 / SU ML: 0.029 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.037
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.166 4025 5.043 %
Rwork0.1422 75785 -
all0.143 --
obs-79810 99.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.006 Å20.003 Å20 Å2
2--0.006 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.22→38.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 49 150 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122389
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162272
X-RAY DIFFRACTIONr_angle_refined_deg1.931.8183259
X-RAY DIFFRACTIONr_angle_other_deg0.6651.7545217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.925301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.009528
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.15351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68210378
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0610106
X-RAY DIFFRACTIONr_chiral_restr0.1010.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02571
X-RAY DIFFRACTIONr_nbd_refined0.2240.2444
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.22116
X-RAY DIFFRACTIONr_nbtor_refined0.180.21174
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2113
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.246
X-RAY DIFFRACTIONr_nbd_other0.2090.2164
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0640.21
X-RAY DIFFRACTIONr_mcbond_it3.9871.3511163
X-RAY DIFFRACTIONr_mcbond_other3.9831.3511163
X-RAY DIFFRACTIONr_mcangle_it5.7392.4341462
X-RAY DIFFRACTIONr_mcangle_other5.7372.4341463
X-RAY DIFFRACTIONr_scbond_it6.3521.6371226
X-RAY DIFFRACTIONr_scbond_other6.3531.6381227
X-RAY DIFFRACTIONr_scangle_it8.7952.8771791
X-RAY DIFFRACTIONr_scangle_other8.7922.8781792
X-RAY DIFFRACTIONr_lrange_it11.89115.622658
X-RAY DIFFRACTIONr_lrange_other11.8915.6242659
X-RAY DIFFRACTIONr_rigid_bond_restr3.90834661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.22-1.2520.312720.28155770.28258490.9310.9391000.281
1.252-1.2860.2812710.25754060.25856770.9420.951000.256
1.286-1.3230.2762670.24452510.24555180.9450.9571000.24
1.323-1.3640.2492690.22851110.22953810.9550.96299.98140.224
1.364-1.4090.2512470.21249990.21352460.9570.9681000.203
1.409-1.4580.2162500.17448370.17650870.9690.9791000.16
1.458-1.5130.2012560.15245740.15548310.9750.98499.97930.134
1.513-1.5750.1752400.12744670.1347070.9810.9891000.109
1.575-1.6440.1442400.10843000.1145400.9860.9921000.091
1.644-1.7250.1562170.10341000.10643180.9850.99399.97680.086
1.725-1.8180.142120.09539200.09741320.9880.9941000.079
1.818-1.9280.1211940.07936870.08138810.9910.9961000.067
1.928-2.060.1272010.09334850.09536860.990.9941000.081
2.06-2.2250.1311690.09832680.09934370.9890.9941000.087
2.225-2.4360.1181490.09830030.09931520.9920.9941000.09
2.436-2.7230.1441550.11527280.11728830.9870.9921000.109
2.723-3.1410.1591380.1424220.14125620.9830.98999.92190.136
3.141-3.8410.1481180.15920590.15821780.9870.98599.95410.161
3.841-5.4060.1641030.14216250.14317300.9870.98999.88440.156
5.406-38.8530.204570.2469660.24410270.9810.96499.61050.263

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