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- PDB-5eub: Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosph... -

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Basic information

Entry
Database: PDB / ID: 5eub
TitleCrystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 2-amino-MTA and sulfate
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTransferase/Transferase Substrate / phosphorylase / Transferase-Transferase Substrate complex
Function / homology
Function and homology information


Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation ...Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5S7 / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsCameron, S.A. / Firestone, R.S. / Schramm, V.L. / Almo, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)6-RO1-CA135405-08 United States
CitationJournal: To be published
Title: Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 2-amino-MTA and sulfate
Authors: Firestone, R.S. / Cameron, S.A. / Tyler, P.C. / Schramm, V.L.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,8437
Polymers33,1191
Non-polymers7246
Water3,243180
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)101,52921
Polymers99,3573
Non-polymers2,17218
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 area9650 Å2
ΔGint-192 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.504, 121.504, 45.328
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-302-

SO4

31A-304-

CL

41A-564-

HOH

51A-570-

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 / MTAPase


Mass: 33119.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTAP, MSAP / Plasmid: pJexpress414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase

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Non-polymers , 5 types, 186 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-5S7 / (2~{R},3~{R},4~{S},5~{S})-2-[2,6-bis(azanyl)purin-9-yl]-5-(methylsulfanylmethyl)oxolane-3,4-diol / 2-amino-5'-deoxy-5'-(methylthio)adenosine


Mass: 312.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N6O3S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.82 % / Description: hexagonal rod
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Protein 15 mg/mL, Reservoir 0.2 M magnesium chloride, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 31, 2015
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35008 / % possible obs: 98.7 % / Redundancy: 6 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Χ2: 1.534 / Net I/av σ(I): 23.42 / Net I/σ(I): 9.5 / Num. measured all: 209976
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.835.90.7382.2717190.8740.3250.8090.87399.8
1.83-1.865.80.63217790.8950.2810.6940.917100
1.86-1.95.80.50717360.920.2250.5560.97799.4
1.9-1.945.80.38617570.940.1710.4230.963100
1.94-1.985.70.36317620.9440.1640.41.03599.6
1.98-2.035.70.29517270.9590.1320.3251.0999.4
2.03-2.085.70.2517440.9650.1130.2751.09598.6
2.08-2.135.70.21917360.9730.0990.2421.21998.8
2.13-2.25.60.20117390.9730.0920.2221.2998.2
2.2-2.275.60.16417320.9790.0750.1811.36997.7
2.27-2.355.50.16217280.9820.0750.181.3998.3
2.35-2.445.60.14817090.9820.0680.1641.39297
2.44-2.555.50.12417140.9860.0560.1371.63597.1
2.55-2.695.40.12117320.9850.0550.1341.88896.8
2.69-2.865.50.12317200.9860.0560.1362.39497.2
2.86-3.085.40.11517550.9860.0530.1272.77198.4
3.08-3.395.70.10417600.9870.0460.1142.5899.5
3.39-3.886.20.07117970.9940.0310.0782.16899.9
3.88-4.887.50.05918070.9960.0230.0641.856100
4.88-5010.10.05918550.9970.020.0621.63298.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREP11.3.02phasing
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K27

1k27


Resolution: 1.81→25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1909 / WRfactor Rwork: 0.1645 / FOM work R set: 0.8436 / SU B: 2.31 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0967 / SU Rfree: 0.0938 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.094 / SU Rfree Cruickshank DPI: 0.0938 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 1701 4.9 %RANDOM
Rwork0.1691 ---
obs0.1703 33251 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.59 Å2 / Biso mean: 25.86 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.57 Å2-0 Å2
2---1.14 Å20 Å2
3---3.7 Å2
Refinement stepCycle: final / Resolution: 1.81→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 44 180 2296
Biso mean--30.22 33.7 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192169
X-RAY DIFFRACTIONr_bond_other_d0.0020.022083
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9772946
X-RAY DIFFRACTIONr_angle_other_deg0.9223.0014801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00123.79779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52115372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.471512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
X-RAY DIFFRACTIONr_mcbond_it1.4352.4231093
X-RAY DIFFRACTIONr_mcbond_other1.4332.421092
X-RAY DIFFRACTIONr_mcangle_it2.1843.6241366
LS refinement shellResolution: 1.81→1.853 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 116 -
Rwork0.252 2423 -
all-2539 -
obs--98.87 %

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