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- PDB-5tc7: Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosph... -

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Basic information

Entry
Database: PDB / ID: 5tc7
TitleCrystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 5'-methylthiotubercidin at 1.75 angstrom
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTransferase/Transferase Inhibitor / phosphorylase / inhibitor / 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-MTH / PHOSPHATE ION / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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)33,7366
Polymers33,1191
Non-polymers6175
Water3,405189
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)101,20718
Polymers99,3573
Non-polymers1,85015
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 area10810 Å2
ΔGint-123 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.359, 123.359, 44.499
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-

PO4

21A-302-

PO4

31A-305-

CL

41A-557-

HOH

51A-575-

HOH

61A-587-

HOH

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Components

#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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MTH / 2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-METHYLSULFANYLMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 5'-DEOXY-5'-(METHYLTHIO)-TUBERCIDIN


Mass: 296.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N4O3S
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.95 Å3/Da / Density % sol: 58.32 % / Description: hexagonal rod
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (15 mg/mL); Reservoir (0.2 M lithium sulfate, 0.1 M TRIS pH 8.5 and 20% (w/v) PEG 4000)

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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: Feb 13, 2015
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 39581 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 11.07 % / Biso Wilson estimate: 29.869 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.087 / Χ2: 0.978 / Net I/σ(I): 18.64 / Num. measured all: 437972
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.74-1.8511.130.9120.7293.0970116639563020.76598.5
1.85-1.980.9640.4175.6366950598259790.43899.9
1.98-2.140.9870.2459.9662289559255810.25799.8
2.14-2.340.9940.15915.4856979517351490.16799.5
2.34-2.610.9960.11220.8951238466446420.11799.5
2.61-3.020.9980.07928.9745503413341220.08299.7
3.02-3.690.9990.05637.5939035352635250.059100
3.69-5.20.9990.04247.3130126275527540.044100
5.20.9990.03445.9615736160115270.03595.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K27

1k27


Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1741 / WRfactor Rwork: 0.1615 / FOM work R set: 0.8728 / SU B: 1.896 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0877 / SU Rfree: 0.0825 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.082 / SU Rfree Cruickshank DPI: 0.0825 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1843 1965 5 %RANDOM
Rwork0.1695 ---
obs0.1702 37326 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.24 Å2 / Biso mean: 27.994 Å2 / Biso min: 14.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å2-0 Å2
3----1.61 Å2
Refinement stepCycle: final / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 36 189 2321
Biso mean--28.39 37.2 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192205
X-RAY DIFFRACTIONr_bond_other_d0.0020.022137
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9762994
X-RAY DIFFRACTIONr_angle_other_deg0.9573.0014932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1255278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51923.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7415393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6581514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
X-RAY DIFFRACTIONr_mcbond_it1.7682.631097
X-RAY DIFFRACTIONr_mcbond_other1.7662.6261096
X-RAY DIFFRACTIONr_mcangle_it2.9173.9331371
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 144 -
Rwork0.24 2730 -
all-2874 -
obs--100 %

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