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- PDB-5tc6: Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosph... -

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Basic information

Entry
Database: PDB / ID: 5tc6
TitleCrystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with propylthio-immucillin-A
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / phosphorylase / inhibitor / complex / TRANSFERASE-TRANSFERASE INHIBITOR 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-7A6 / PHOSPHATE ION / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 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: TBA
Authors: Firestone, R.S. / Cameron, S.A. / Karp, J.M. / Arcus, V.L. / Schramm, V.L.
History
DepositionSep 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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)33,6886
Polymers33,1191
Non-polymers5695
Water3,999222
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)101,06418
Polymers99,3573
Non-polymers1,70715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8810 Å2
ΔGint-119 kcal/mol
Surface area29270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.760, 122.760, 44.484
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-304-

NA

21A-305-

CL

31A-588-

HOH

41A-605-

HOH

51A-609-

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 , 6 types, 227 molecules

#2: Chemical ChemComp-7A6 / (2S,3S,4R,5S)-2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-[(propylsulfanyl)methyl]pyrrolidine-3,4-diol


Mass: 323.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N5O2S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 57.9 % / Description: rod
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (15 mg/mL); Reservoir (0.17 M sodium acetate, 85 mM Tris:HCl (pH 8.5), 25% (w/v) PEG 4000 and 15% (v/v) glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2014
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 64277 / % possible obs: 100 % / Redundancy: 11.5 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.024 / Rrim(I) all: 0.083 / Χ2: 1.296 / Net I/av σ(I): 35.31 / Net I/σ(I): 10.2 / Num. measured all: 738369
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.48-1.5110.70.87630.8251100
1.51-1.5311.10.7030.8851100
1.53-1.56110.6040.9131100
1.56-1.5911.10.5520.9281100
1.59-1.6311.10.4470.9451100
1.63-1.6711.20.3880.961100
1.67-1.7111.20.3480.9691100
1.71-1.7511.30.3020.9751100
1.75-1.8111.30.2550.9811100
1.81-1.8611.40.2040.9881100
1.86-1.9311.40.1730.9911100
1.93-2.0111.50.1410.9931100
2.01-2.111.60.1190.9951100
2.1-2.2111.70.0990.9951100
2.21-2.3511.80.0910.9971100
2.35-2.5311.90.0880.9971100
2.53-2.7912.20.0810.9971100
2.79-3.1912.10.0630.9981100
3.19-4.0211.90.0410.9991100
4.02-5012.10.0340.999199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K27

1k27


Resolution: 1.48→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.914 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0548 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.056 / SU Rfree Cruickshank DPI: 0.0556 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 3177 4.9 %RANDOM
Rwork0.1671 ---
obs0.168 61028 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.86 Å2 / Biso mean: 19.003 Å2 / Biso min: 9.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.48→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 35 222 2362
Biso mean--16.11 30.89 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192263
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9773084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08724.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00415411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3261514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211653
X-RAY DIFFRACTIONr_mcbond_it0.9831.6541116
X-RAY DIFFRACTIONr_mcangle_it1.6982.4771401
X-RAY DIFFRACTIONr_scbond_it1.491.8681145
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 236 -
Rwork0.234 4450 -
all-4686 -
obs--99.96 %

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