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- PDB-9u79: Crystal structure of MTAP from Aeropyrum pernix complex with MTA ... -

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Basic information

Entry
Database: PDB / ID: 9u79
TitleCrystal structure of MTAP from Aeropyrum pernix complex with MTA at 100K, Soaked in potassium phosphate pH7.0 with MTA
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 / : / 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: 1.19 Å
AuthorsIizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 100K, Soaked in potassium phosphate pH7.0 with MTA
Authors: Iizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.
History
DepositionMar 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: 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)31,6827
Polymers30,7771
Non-polymers9056
Water2,378132
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)95,04721
Polymers92,3323
Non-polymers2,71518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area12880 Å2
ΔGint-37 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.66, 77.66, 230.798
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein S-methyl-5'-thioadenosine phosphorylase


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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YAQ8

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Non-polymers , 5 types, 138 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.17883253 Å3/Da / Density % sol: 43.58209 %
Crystal growTemperature: 293 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, 0.1M phosphate citrate pH5.4, 5mM MTA. Crystals soaked in 0.1M potassium phosphate pH7.0 with 5mM 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: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.19→43.79 Å / Num. obs: 86141 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.026 / Rrim(I) all: 0.06 / Χ2: 0.96 / Net I/σ(I): 21.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
6.52-43.798.80.01593.660110.0070.0160.6199.1
1.19-1.219.90.5973.142340.6650.2940.6660.63100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WTA

1wta


Resolution: 1.19→43.79 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.084 / SU ML: 0.021 / Cross valid method: FREE R-VALUE / ESU R: 0.031 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1572 4322 5.018 %
Rwork0.1299 81804 -
all0.131 --
obs-86126 99.967 %
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: 16.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.143 Å20.071 Å20 Å2
2--0.143 Å20 Å2
3----0.464 Å2
Refinement stepCycle: LAST / Resolution: 1.19→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 59 133 2334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122285
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162181
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.8183109
X-RAY DIFFRACTIONr_angle_other_deg0.6891.7525011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.915284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.308526
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.12351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16210361
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.88510101
X-RAY DIFFRACTIONr_chiral_restr0.1090.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02536
X-RAY DIFFRACTIONr_nbd_refined0.2190.2409
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21966
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21122
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2100
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1150.228
X-RAY DIFFRACTIONr_nbd_other0.1910.2131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0830.222
X-RAY DIFFRACTIONr_mcbond_it4.5651.3631103
X-RAY DIFFRACTIONr_mcbond_other4.561.3631103
X-RAY DIFFRACTIONr_mcangle_it6.5212.4611380
X-RAY DIFFRACTIONr_mcangle_other6.5192.4611381
X-RAY DIFFRACTIONr_scbond_it7.2271.7151182
X-RAY DIFFRACTIONr_scbond_other7.2241.7161183
X-RAY DIFFRACTIONr_scangle_it10.0142.9831723
X-RAY DIFFRACTIONr_scangle_other10.0112.9851724
X-RAY DIFFRACTIONr_lrange_it12.5415.0212491
X-RAY DIFFRACTIONr_lrange_other12.48114.8362476
X-RAY DIFFRACTIONr_rigid_bond_restr4.28934466
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
1.19-1.2210.2553110.24160160.24163270.9560.961000.224
1.221-1.2540.2373030.2258450.22161480.9590.9641000.203
1.254-1.2910.2032840.18656860.18759700.9720.9741000.168
1.291-1.330.2032750.17155300.17258050.9690.9781000.151
1.33-1.3740.1832760.15653760.15756520.9750.9821000.137
1.374-1.4220.1712610.13751590.13954200.9790.9871000.116
1.422-1.4760.1442780.11250150.11452930.9860.9911000.093
1.476-1.5360.1292510.10348320.10550830.9890.9931000.086
1.536-1.6040.1312690.09545960.09748650.9890.9941000.079
1.604-1.6820.1442290.09344520.09546820.9880.99599.97860.077
1.682-1.7730.1332070.09342280.09544360.9890.99599.97750.079
1.773-1.8810.1292390.09339650.09542060.990.99599.95240.079
1.881-2.010.1392150.09637550.09839720.9890.99499.94960.084
2.01-2.1710.1422030.10435110.10637150.9890.99499.97310.094
2.171-2.3770.1311790.10632120.10733930.9910.99499.94110.098
2.377-2.6570.1211440.10829640.10831110.990.99399.90360.101
2.657-3.0660.1491510.12926050.1327560.9870.991000.124
3.066-3.7510.1661190.14922340.1523550.9840.98799.91510.149
3.751-5.2850.149790.13817800.13818630.9880.98999.78530.145
5.285-43.790.272490.20810430.21110990.9680.97799.36310.216

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