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- PDB-5fak: Crystal structure of Double Mutant S12T and N87T of Adenosine/Met... -

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Basic information

Entry
Database: PDB / ID: 5fak
TitleCrystal structure of Double Mutant S12T and N87T of Adenosine/Methylthioadenosine Phosphorylase from Schistosoma mansoni in complex with Adenine
ComponentsMethylthioadenosine phosphorylase
KeywordsTRANSFERASE
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 / nucleus / 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
ADENINE / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsTorini, J.R. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474402/2013-4 Brazil
CitationJournal: PLoS Negl Trop Dis / Year: 2016
Title: Crystal Structure of Schistosoma mansoni Adenosine Phosphorylase/5'-Methylthioadenosine Phosphorylase and Its Importance on Adenosine Salvage Pathway.
Authors: Torini, J.R. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.D.
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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

Downloads & links

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Assembly

Deposited unit
A: Methylthioadenosine phosphorylase
B: Methylthioadenosine phosphorylase
C: Methylthioadenosine phosphorylase
D: Methylthioadenosine phosphorylase
E: Methylthioadenosine phosphorylase
F: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,68016
Polymers211,5636
Non-polymers1,11710
Water23,0051277
1
A: Methylthioadenosine phosphorylase
B: Methylthioadenosine phosphorylase
C: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3408
Polymers105,7823
Non-polymers5585
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-97 kcal/mol
Surface area30750 Å2
MethodPISA
2
D: Methylthioadenosine phosphorylase
E: Methylthioadenosine phosphorylase
F: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3408
Polymers105,7823
Non-polymers5585
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-93 kcal/mol
Surface area31280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.060, 82.090, 150.150
Angle α, β, γ (deg.)90.000, 101.230, 90.000
Int Tables number4
Space group name H-MP1211
DetailsTrimer confirmed by gel filtration

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Components

#1: Protein
Methylthioadenosine phosphorylase


Mass: 35260.508 Da / Num. of mol.: 6 / Mutation: S12T,N87T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I0B503, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1277 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM Bris-tris or Mes, 14-18% PEG3350, pH 6.5 / PH range: 6.1-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.87→79.51 Å / Num. obs: 155607 / % possible obs: 97.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.43 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
1.87-1.924.41.11096.6
8.36-79.514.10.031094.9

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F77

5f77


Resolution: 1.87→79.508 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 7588 4.88 %Random selection
Rwork0.1811 147944 --
obs0.1827 155532 97.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.9 Å2 / Biso mean: 36.5346 Å2 / Biso min: 14.56 Å2
Refinement stepCycle: final / Resolution: 1.87→79.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12897 0 70 1277 14244
Biso mean--44.21 42.07 -
Num. residues----1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513249
X-RAY DIFFRACTIONf_angle_d0.74217995
X-RAY DIFFRACTIONf_chiral_restr0.052091
X-RAY DIFFRACTIONf_plane_restr0.0052299
X-RAY DIFFRACTIONf_dihedral_angle_d15.7117894
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.87-1.89130.37852700.33474832510297
1.8913-1.91350.32462180.30524866508496
1.9135-1.93680.33862230.29624877510096
1.9368-1.96140.3052530.27434874512796
1.9614-1.98720.29312470.25754903515097
1.9872-2.01440.28852430.25384854509797
2.0144-2.04320.29752530.23764870512397
2.0432-2.07370.282440.22894885512997
2.0737-2.10610.25192390.21234895513497
2.1061-2.14060.25152310.21314942517397
2.1406-2.17750.27032450.20684926517197
2.1775-2.21710.2642450.19524868511397
2.2171-2.25980.23942940.194907520197
2.2598-2.30590.20482510.18234888513998
2.3059-2.3560.23012080.18194974518298
2.356-2.41090.22832440.1824953519797
2.4109-2.47110.21672450.18394912515798
2.4711-2.5380.2382590.17974931519098
2.538-2.61270.21642700.17644930520098
2.6127-2.6970.2282560.18044971522798
2.697-2.79340.2242760.17214940521698
2.7934-2.90520.20282530.17594952520598
2.9052-3.03750.22962970.18194920521798
3.0375-3.19760.19642640.1814993525798
3.1976-3.39790.19872520.17535018527098
3.3979-3.66030.212450.16734998524399
3.6603-4.02860.18012630.14665004526799
4.0286-4.61150.14672480.12795050529898
4.6115-5.80980.17052520.15525052530498
5.8098-79.57990.2063000.18764959525996
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)
15.1818-2.034-2.30184.9907-4.17437.15340.3562-0.25950.31440.7105-0.04730.4188-0.39770.0561-0.12270.2904-0.07480.0980.2277-0.01390.427-17.3536-19.908472.4259
21.58180.7719-0.25622.5773-0.44431.61940.0602-0.0784-0.23190.1165-0.07720.27790.2472-0.18940.02550.2244-0.02780.04560.19290.01620.3076-9.8352-22.163669.0482
32.8336-0.8235-0.60721.79850.59131.81180.03310.19190.0288-0.0848-0.08540.194-0.0891-0.22380.05520.19150.02680.00690.2030.02270.1855-9.0034-7.405658.587
42.85450.89290.18641.7006-0.03171.41380.1108-0.15490.10720.063-0.06720.2006-0.0304-0.2146-0.03580.20970.04560.02670.17560.02350.2093-6.5959-8.996663.2747
51.4791-3.3346-1.76357.5153.60764.4338-0.26230.628-0.97970.0046-0.22010.84540.6275-0.4140.51880.3389-0.03980.00210.3508-0.06880.322613.3868-33.474830.0229
61.8143-0.7499-0.85691.2880.29892.613-0.10810.1058-0.4250.0763-0.03940.06670.3733-0.0910.13070.290.00040.0360.2138-0.03430.287415.4679-32.604338.7926
71.0608-0.2367-0.17640.84790.50041.37860.11390.18990.088-0.1704-0.0944-0.0002-0.1766-0.1135-0.01620.27090.04110.03920.20310.0110.172412.7465-15.013237.7868
84.22121.33881.7992.26742.03724.9656-0.27160.089-0.3716-0.3967-0.11850.5290.611-0.32180.0350.65430.11980.17620.60860.0840.4518-4.8532-15.638736.6202
90.9529-0.2605-0.6621.21620.72293.0840.06810.4074-0.1692-0.2301-0.0502-0.06930.00130.3409-0.09190.31950.06860.07740.21570.02130.245723.0298-23.227531.615
101.5890.25971.15543.1784-0.08842.05150.0515-0.1059-0.2988-0.0116-0.0917-0.52420.09480.45730.02280.2230.01930.01050.29630.03360.321534.5437-15.702473.6836
111.1020.082-0.10711.4088-0.23560.78260.0481-0.06350.04810.0092-0.0139-0.0523-0.07730.0776-0.0370.2369-0.0070.02090.1904-0.00270.201125.2816-6.277568.5419
120.8956-0.0551-0.11020.91340.7831.29530.0290.08920.1187-0.23820.0237-0.0845-0.19080.0409-0.05690.23320.00440.02690.16250.02340.194122.2608-3.27957.6012
131.65730.14290.1851.73810.10646.68210.03360.4780.0608-0.4920.075-0.0589-0.28760.0346-0.09320.4021-0.04420.0760.2905-0.01730.305828.5293-2.326454.7057
143.5304-0.3372-2.40593.47781.65052.27590.10770.03630.1468-0.42160.2346-0.465-0.10430.4257-0.29710.2874-0.04950.02750.21360.02110.327140.1265-1.737563.1067
153.63254.67331.36696.13831.35091.94970.1777-0.5538-0.10430.5208-0.21370.1435-0.1086-0.27820.04340.42550.00440.09490.25210.01220.242115.392-4.319583.6466
163.9498-0.1060.91754.8952-2.9351.93270.3522-0.03140.25390.8104-0.17090.8387-0.1972-0.2541-0.03580.3342-0.04450.15370.3817-0.01690.4531-30.1671-21.9616146.4492
171.8780.0801-0.6662.4298-0.721.91920.01-0.0955-0.45720.1778-0.02630.33780.3033-0.22970.0430.2388-0.04750.0250.22780.03450.3519-24.0936-24.1853142.4976
183.0253-0.6817-0.65211.7360.2282.01780.02850.1316-0.07-0.0776-0.05580.1367-0.143-0.26970.0130.18090.0393-0.01380.19940.01580.1515-24.5046-9.3268131.974
193.18530.6433-0.28911.6971-0.42891.55980.1278-0.0763-0.03730.0718-0.05390.2195-0.0916-0.1833-0.06540.23330.04620.01390.21180.02890.2396-21.9369-11.3649136.1205
201.3672-3.0549-1.11156.82363.09195.1385-0.26530.2304-0.7326-0.0709-0.2050.8760.6131-0.30010.41990.3474-0.00750.04170.3391-0.08310.396-1.8035-34.133102.5743
211.2016-0.35-0.34791.79770.12052.9787-0.04020.0945-0.308-0.053-0.05940.12220.2225-0.00670.10380.22490.0020.05040.2251-0.0470.2553-1.6607-28.3526110.531
220.6994-0.2075-0.42511.51010.38122.25270.02690.1824-0.0783-0.1979-0.1185-0.022-0.1452-0.0830.06950.30190.02540.05390.2635-0.02180.2405-1.6662-18.0921108.7675
231.97470.73242.86461.36260.1155.00160.2032-0.2562-0.30660.2644-0.014-0.66150.62441.428-0.26320.3177-0.0135-0.04040.60470.08350.472122.8998-10.502144.5853
243.7299-0.0693-0.37260.90420.51510.38620.0229-0.9305-0.72310.6195-0.3727-0.6460.1620.85250.29580.38360.0251-0.03360.50120.22150.548215.1608-22.9484147.3943
251.88110.0228-0.40252.3255-0.60061.94510.0311-0.3112-0.18340.1413-0.1449-0.16920.02180.35380.10770.2002-0.02520.02410.280.04810.251813.5311-9.5464139.9179
261.39380.3457-0.31161.27290.00011.19850.0926-0.09580.0025-0.0091-0.0219-0.0473-0.14410.1176-0.06370.2248-0.01450.02120.22680.01620.2296.2915-3.5614136.1759
273.27310.66681.51743.5773-0.51184.6612-0.05230.4758-0.0287-0.7028-0.0627-0.2124-0.08860.39530.13090.3942-0.03580.10490.30660.01020.366813.2128-2.6505127.3295
283.97421.0912-1.39481.69420.05092.06980.2003-0.58930.07460.1511-0.1295-0.1573-0.20070.414-0.06850.2706-0.0188-0.05830.22080.07810.236714.3915-2.975144.5569
290.5558-0.02310.10750.45880.01080.0196-0.50880.1833-0.3688-0.194-0.38620.02580.3828-0.23280.65160.3044-0.0210.15880.14890.0150.4831-3.7903-9.544383.6694
302.000121.99992.00011.99982.0001-0.47-0.27920.03460.99871.1619-0.22341.08871.4474-0.6931.1631-0.09820.4750.9586-0.37310.6869-14.5499-18.9195113.7893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 90 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 182 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 290 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 23 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 91 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 92 through 231 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 232 through 249 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 250 through 291 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 3 through 38 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 39 through 164 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 165 through 220 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 221 through 242 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 243 through 269 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 270 through 293 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 4 through 26 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 27 through 90 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 91 through 182 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 183 through 291 )D0
20X-RAY DIFFRACTION20chain 'E' and (resid 3 through 23 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 24 through 110 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 111 through 290 )E0
23X-RAY DIFFRACTION23chain 'F' and (resid 3 through 23 )F0
24X-RAY DIFFRACTION24chain 'F' and (resid 24 through 38 )F0
25X-RAY DIFFRACTION25chain 'F' and (resid 39 through 110 )F0
26X-RAY DIFFRACTION26chain 'F' and (resid 111 through 220 )F0
27X-RAY DIFFRACTION27chain 'F' and (resid 221 through 242 )F0
28X-RAY DIFFRACTION28chain 'F' and (resid 243 through 291 )F0
29X-RAY DIFFRACTION29(chain 'A' and resid 301) or (chain 'B' and resid 301) or (chain 'D' and resid 301)G0
30X-RAY DIFFRACTION30chain 'E' and (resid 301 through 301 )G0

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