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- PDB-9lr4: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 9lr4
TitleCrystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 343K
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
ADENINE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 343K
Authors: Iizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.
History
DepositionJan 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 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)31,1144
Polymers30,7771
Non-polymers3363
Water81145
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)93,34112
Polymers92,3323
Non-polymers1,0099
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area9280 Å2
ΔGint-54 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.044, 79.044, 233.312
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32

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Components

#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
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 2.28176999 Å3/Da / Density % sol: 46.1279678 %
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

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Data collection

DiffractionMean temperature: 343 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: Nov 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→44.4 Å / Num. obs: 31368 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.046 / Rrim(I) all: 0.105 / Χ2: 1.01 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9-44.337.90.02470.12520.9990.0120.0271.0998.6
1.7-1.739.81.1792.516510.6760.5721.2881.01100

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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: 1.7→44.4 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.859 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1819 1611 5.136 %
Rwork0.1452 29756 -
all0.147 --
obs-31367 99.971 %
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: 27.831 Å2
Baniso -1Baniso -2Baniso -3
1-0.141 Å20.07 Å2-0 Å2
2--0.141 Å2-0 Å2
3----0.456 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 22 45 2209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162186
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.8153164
X-RAY DIFFRACTIONr_angle_other_deg0.6061.7555017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3425293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.727526
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.0751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94910365
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.22110104
X-RAY DIFFRACTIONr_chiral_restr0.090.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
X-RAY DIFFRACTIONr_nbd_refined0.220.2362
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21901
X-RAY DIFFRACTIONr_nbtor_refined0.180.21138
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21250
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3090.221
X-RAY DIFFRACTIONr_nbd_other0.2230.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0610.28
X-RAY DIFFRACTIONr_mcbond_it2.7842.2761145
X-RAY DIFFRACTIONr_mcbond_other2.7842.2761145
X-RAY DIFFRACTIONr_mcangle_it4.0654.0741435
X-RAY DIFFRACTIONr_mcangle_other4.0644.0751436
X-RAY DIFFRACTIONr_scbond_it5.1613.051174
X-RAY DIFFRACTIONr_scbond_other5.1613.051174
X-RAY DIFFRACTIONr_scangle_it8.2375.2291725
X-RAY DIFFRACTIONr_scangle_other8.2345.2281726
X-RAY DIFFRACTIONr_lrange_it10.34325.4012428
X-RAY DIFFRACTIONr_lrange_other10.34625.4152425
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
1.7-1.7440.2611140.23921560.2422710.9540.9699.9560.222
1.744-1.7920.2351190.22921250.22922440.9640.9641000.208
1.792-1.8440.2691090.20720740.2121830.9580.971000.182
1.844-1.90.211140.18319730.18420880.970.97799.95210.154
1.9-1.9630.1611130.15419300.15520430.980.9841000.129
1.963-2.0310.21230.17218650.17419880.9740.9811000.144
2.031-2.1080.177960.15918190.1619150.9790.9841000.137
2.108-2.1940.174950.14117570.14218520.9810.9881000.122
2.194-2.2910.185920.14316640.14517560.980.9881000.123
2.291-2.4020.164870.12616150.12817020.9820.9911000.109
2.402-2.5320.174700.12515400.12716100.9810.9911000.106
2.532-2.6850.187860.13814530.14115390.980.9881000.121
2.685-2.870.176760.13813700.1414460.980.9891000.123
2.87-3.0990.191710.13712790.1413500.9770.9881000.126
3.099-3.3930.178590.12811830.1312440.9840.98999.83920.12
3.393-3.790.129600.1310920.1311520.990.991000.129
3.79-4.3710.133400.1099670.1110070.9880.9921000.114
4.371-5.3410.136280.1138390.1148670.9870.9931000.123
5.341-7.4990.172290.1696650.1696940.9870.9831000.181
7.499-44.40.292300.1763900.1824220.9350.97799.52610.198

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