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

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Basic information

Entry
Database: PDB / ID: 9jhv
TitleCrystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 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
5'-DEOXY-5'-METHYLTHIOADENOSINE / 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: 1.65 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 353K
Authors: Iizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.
History
DepositionSep 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)31,2764
Polymers30,7771
Non-polymers4983
Water99155
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)93,82712
Polymers92,3323
Non-polymers1,4959
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 area10250 Å2
ΔGint-74 kcal/mol
Surface area27840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.854, 78.854, 233.369
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.27136 Å3/Da / Density % sol: 45.8812599 %
Crystal growTemperature: 293.2 K / Method: counter-diffusion
Details: he 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: he 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: 343 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: 1.65→44.36 Å / Num. obs: 34102 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.068 / Rrim(I) all: 0.157 / Χ2: 1.02 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.04-44.367.90.05230.72420.9970.0260.0590.9698.6
1.65-1.68102.4691.116790.3391.2032.7521.05100

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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: 1.65→44.36 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.975 / SU B: 4.047 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1674 1788 5.243 %
Rwork0.1182 32313 -
all0.121 --
obs-34101 99.953 %
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: 28.908 Å2
Baniso -1Baniso -2Baniso -3
1--0.329 Å2-0.165 Å2-0 Å2
2---0.329 Å2-0 Å2
3---1.067 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 32 55 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122251
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162124
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.8193069
X-RAY DIFFRACTIONr_angle_other_deg0.581.7584874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.961526
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.05751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07210356
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.78210101
X-RAY DIFFRACTIONr_chiral_restr0.0850.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_nbd_refined0.2150.2355
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21831
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21105
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.256
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.30.225
X-RAY DIFFRACTIONr_nbd_other0.210.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0580.216
X-RAY DIFFRACTIONr_mcbond_it6.8322.4281103
X-RAY DIFFRACTIONr_mcbond_other6.8222.4281103
X-RAY DIFFRACTIONr_mcangle_it10.2454.3641381
X-RAY DIFFRACTIONr_mcangle_other10.2424.3641382
X-RAY DIFFRACTIONr_scbond_it11.0423.121148
X-RAY DIFFRACTIONr_scbond_other11.0413.121148
X-RAY DIFFRACTIONr_scangle_it16.4265.4261687
X-RAY DIFFRACTIONr_scangle_other16.4215.4251688
X-RAY DIFFRACTIONr_lrange_it19.60524.6442357
X-RAY DIFFRACTIONr_lrange_other19.60124.652358
X-RAY DIFFRACTIONr_rigid_bond_restr4.0334375
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
1.65-1.6930.2691340.26423470.26424830.9560.94899.91940.265
1.693-1.7390.2711170.25123190.25224380.9470.95499.9180.251
1.739-1.790.2631370.2222240.22223610.9550.9671000.216
1.79-1.8450.2371330.19521570.19722900.9610.9751000.187
1.845-1.9050.1921270.15620880.15822150.9730.9841000.145
1.905-1.9720.1941130.12420550.12821680.9780.991000.112
1.972-2.0460.171010.10819700.11120710.9830.9931000.096
2.046-2.1290.1651090.10619020.10920110.9850.9941000.095
2.129-2.2240.161050.09517950.09819000.9840.9951000.086
2.224-2.3320.134970.08917560.09118530.990.9961000.08
2.332-2.4580.14960.08916800.09217770.9880.99699.94370.079
2.458-2.6060.157950.09515690.09816640.9860.9951000.086
2.606-2.7860.169730.1114890.11315630.9850.99399.9360.102
2.786-3.0080.165780.10813980.11114760.9830.9931000.103
3.008-3.2930.139720.10212850.10413570.9890.9931000.1
3.293-3.680.15550.10111720.10312280.9870.99499.91860.102
3.68-4.2440.119470.09110580.09211050.9910.9951000.099
4.244-5.1860.121430.0949000.0959430.9940.9951000.106
5.186-7.2840.203370.1317140.1347520.9840.99199.8670.145
7.284-44.360.243190.154350.1534590.9780.98298.91070.168

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