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- PDB-5tc5: Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosph... -

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Basic information

Entry
Database: PDB / ID: 5tc5
TitleCrystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with butylthio-DADMe-Immucillin-A and chloride
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-BIG / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: S-methyl-5'-thioadenosine phosphorylase
C: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,50510
Polymers99,3573
Non-polymers1,1487
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-71 kcal/mol
Surface area31510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.522, 121.927, 192.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA9 - 27923 - 293
21BB9 - 27923 - 293
12AA9 - 27923 - 293
22CC9 - 27923 - 293
13BB9 - 28023 - 294
23CC9 - 28023 - 294

NCS ensembles :
ID
1
2
3

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Components

#1: Protein S-methyl-5'-thioadenosine phosphorylase / / 5'-methylthioadenosine phosphorylase / MTAPase


Mass: 33119.051 Da / Num. of mol.: 3
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-BIG / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol / butylthio-DADMe-Immucillin A


Mass: 335.468 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H25N5OS
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.64 Å3/Da / Density % sol: 53.48 % / Description: block
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (15 mg/mL); Reservoir (3 M sodium chloride and 0.1 M sodium acetate (pH 4.5))

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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(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 75649 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.48 % / Biso Wilson estimate: 39.471 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.08 / Χ2: 0.976 / Net I/σ(I): 16.86 / Num. measured all: 566038
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.96-2.087.480.7822.77199
2.08-2.220.4284.951100
2.22-2.40.2717.571100
2.4-2.630.16411.571100
2.63-2.940.09318.761100
2.94-3.390.06427.171100
3.39-4.140.04637.631100
4.14-5.840.03943.61199.9
5.840.03542.77196.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XDSdata scaling
MOLREP11.2.08phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K27

1k27


Resolution: 1.96→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2105 / WRfactor Rwork: 0.1829 / FOM work R set: 0.794 / SU B: 9.035 / SU ML: 0.129 / SU R Cruickshank DPI: 0.1439 / SU Rfree: 0.1308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 3779 5 %RANDOM
Rwork0.1896 ---
obs0.191 71803 99.76 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 147.8 Å2 / Biso mean: 51.803 Å2 / Biso min: 22.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å20 Å2-0 Å2
2--1.54 Å20 Å2
3---0.97 Å2
Refinement stepCycle: final / Resolution: 1.96→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 73 228 6562
Biso mean--36.09 41.94 -
Num. residues----825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196470
X-RAY DIFFRACTIONr_bond_other_d0.0090.026262
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9728767
X-RAY DIFFRACTIONr_angle_other_deg1.605314430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76623.975239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.663151117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1841536
X-RAY DIFFRACTIONr_chiral_restr0.120.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217119
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021371
X-RAY DIFFRACTIONr_mcbond_it2.4921.7193296
X-RAY DIFFRACTIONr_mcbond_other2.4911.7183295
X-RAY DIFFRACTIONr_mcangle_it3.4662.5614110
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A326800.07
12B326800.07
21A324100.06
22C324100.06
31B327080.07
32C327080.07
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 274 -
Rwork0.304 5216 -
all-5490 -
obs--99.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8274-0.00170.27922.8324-0.09722.91180.1322-0.0664-0.14980.29980.02720.19970.5318-0.3539-0.15930.6028-0.0751-0.14480.04530.02480.0944-21.939-57.226-25.438
21.5883-0.20651.31252.79030.30753.031-0.3149-0.24890.17170.6090.03180.0522-0.5095-0.35460.28310.7420.0722-0.1920.051-0.0350.0811-15.167-23.282-12.577
31.45060.54410.72784.2044-1.13872.4358-0.0993-0.13360.2271-0.45870.12810.8383-0.118-0.317-0.02880.55880.028-0.24680.0433-0.00290.2383-30.22-26.042-45.933
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 281
2X-RAY DIFFRACTION2B9 - 280
3X-RAY DIFFRACTION3C9 - 280

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