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- PDB-4l5a: Methylthioadenosine phosphorylase from Schistosoma mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 4l5a
TitleMethylthioadenosine phosphorylase from Schistosoma mansoni in complex with tubercidin
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTRANSFERASE/ANTIBIOTIC / Transferase / phosphorylase / Nucleoside phosphorylase / Enzyme / TRANSFERASE-ANTIBIOTIC complex
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
Chem-TBN / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2993 Å
AuthorsTorini, J.R. / DeMarco, R. / Brandao-Neto, J. / Pereira, H.M.
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
DepositionJun 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
D: S-methyl-5'-thioadenosine phosphorylase
E: S-methyl-5'-thioadenosine phosphorylase
F: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,73118
Polymers211,5576
Non-polymers2,17412
Water10,106561
1
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)106,8659
Polymers105,7783
Non-polymers1,0876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-94 kcal/mol
Surface area30820 Å2
MethodPISA
2
D: S-methyl-5'-thioadenosine phosphorylase
E: S-methyl-5'-thioadenosine phosphorylase
F: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8659
Polymers105,7783
Non-polymers1,0876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-92 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.068, 82.680, 150.558
Angle α, β, γ (deg.)90.000, 101.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35259.480 Da / Num. of mol.: 6 / Fragment: SmMTAP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Strain: BH / Gene: SmMTAP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I0B503, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical
ChemComp-TBN / '2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 7-DEAZAADENOSINE


Mass: 266.253 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H14N4O4
#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.: 561 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Bris-tris or Mes, 14-18% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2011 / Details: DCM
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.299→30 Å / Num. all: 170562 / Num. obs: 158912 / % possible obs: 93.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.749 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.02
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.299-2.440.2363.534873725362192.5
2.44-2.60.1625.054964625324198
2.6-2.810.1087.484546523262196.8
2.81-3.080.06810.894245221681198.1
3.08-3.440.04515.573775719355196.5
3.44-3.960.04219.662216411855167.2
3.96-4.830.02527.22794914409195.9
4.83-6.730.02527.352158211168195.8
6.73-300.01732.35128616496195.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2993→29.2 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8484 / SU ML: 0.24 / σ(F): 1.07 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 7938 5 %Random
Rwork0.1889 ---
all0.1904 170562 --
obs0.1904 158778 93.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.31 Å2 / Biso mean: 37.8519 Å2 / Biso min: 15.56 Å2
Refinement stepCycle: LAST / Resolution: 2.2993→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12861 0 144 561 13566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313266
X-RAY DIFFRACTIONf_angle_d0.79118007
X-RAY DIFFRACTIONf_chiral_restr0.0482086
X-RAY DIFFRACTIONf_plane_restr0.0032286
X-RAY DIFFRACTIONf_dihedral_angle_d12.1234739
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 (%)
2.2993-2.32540.26762050.25533883408872
2.3254-2.35280.28662740.23035292556698
2.3528-2.38150.25962750.20725247552298
2.3815-2.41160.23982820.21255319560198
2.4116-2.44330.28152780.21715291556998
2.4433-2.47680.26052760.20975237551398
2.4768-2.51210.23122840.20085346563098
2.5121-2.54960.27932760.2035231550798
2.5496-2.58940.22092810.20145321560298
2.5894-2.63180.24492810.20745321560298
2.6318-2.67720.27512650.21365045531094
2.6772-2.72580.2462770.20485171544897
2.7258-2.77820.26732760.19645291556798
2.7782-2.83490.26032780.19835368564698
2.8349-2.89650.24192820.20135310559298
2.8965-2.96380.2322770.20455280555798
2.9638-3.03780.26592760.20295258553498
3.0378-3.11990.2332810.20945330561198
3.1199-3.21160.24752820.20725286556898
3.2116-3.31510.23222780.20035261553998
3.3151-3.43340.22282630.20535066532993
3.4334-3.57060.22282530.21284768502189
3.5706-3.73280.26961340.26862521265546
3.7328-3.92920.211830.20773603378667
3.9292-4.17470.20372590.15974779503889
4.1747-4.4960.13852790.13655258553797
4.496-4.94650.16262710.1325196546797
4.9465-5.65770.1762690.16175105537495
5.6577-7.11110.20452750.16925258553397
7.1111-29.20260.15732680.14975198546696
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.66770.7455-1.34351.4673-0.45952.65880.1603-0.0693-0.0075-0.4374-0.1159-0.29320.15040.26090.09190.33310.07230.14390.23130.0010.577740.8645-24.31251.3376
21.8525-0.2282-0.27642.14511.15790.63890.0636-0.0851-0.3343-0.1665-0.1538-0.33950.09580.13630.09670.2454-0.0020.05880.19540.03230.366332.6036-21.15786.0619
32.7089-0.1926-0.35381.4503-0.10371.85270.053-0.3055-0.08430.0745-0.073-0.1876-0.23970.17760.05110.2086-0.0359-0.01950.1958-0.02350.197334.7246-9.107314.9958
42.64420.0296-0.11180.16890.28591.23750.10430.02990.0134-0.0144-0.04090.006-0.25870.0152-0.03080.2702-0.04330.03170.1851-0.0240.278825.739-7.711210.7258
51.68780.613-0.54342.3748-0.68853.001-0.17230.0014-0.3576-0.2020.071-0.2763-0.06080.25410.07140.25340.00920.03690.2915-0.04640.401841.2126-15.619411.1513
61.52182.3285-1.01133.7755-1.00942.18790.1822-0.7246-0.8120.3717-0.1526-0.43360.14210.0837-0.00690.3426-0.087-0.04370.39910.13210.323212.0542-34.838242.9224
71.14420.64-0.62551.5703-0.181.71580.0104-0.2724-0.41990.0235-0.1381-0.06790.39980.10840.10340.2682-0.0376-0.01020.23230.07590.312310.0567-34.309134.5385
81.9660.19240.28211.1578-0.53262.36110.1659-0.31890.0990.2188-0.1657-0.1496-0.37590.10960.00210.2328-0.0811-0.01190.20120.00950.190210.9445-16.488237.7676
93.2339-2.9839-2.01722.83961.45533.2431-0.1290.09760.23580.29850.086-0.1802-0.16710.47240.07310.2621-0.13380.00630.27070.02810.276624.7539-11.749426.3166
101.80030.00050.09781.2428-0.10272.30570.1522-0.3655-0.10730.1952-0.1318-0.1025-0.02330.1908-0.03060.2781-0.08080.0090.2430.03380.17810.4554-22.084538.872
111.9079-0.00973.06661.42740.46345.10350.1679-0.0815-0.1596-0.06820.01330.4046-0.0561-0.8765-0.11160.20710.05310.01750.3373-0.00050.306-11.9476-11.75360.2607
122.39381.4453-1.5273.30290.5431.8922-0.2660.6041-0.2641-0.69310.21590.44690.1283-0.47260.00340.3267-0.0467-0.04810.4152-0.08760.3779-4.5887-23.9896-2.2507
130.97670.469-0.04191.5754-0.0852.51560.02290.1745-0.0305-0.21090.02540.09120.0969-0.1194-0.07780.20550.02830.00610.158-0.0120.2056-4.7414-14.61281.9611
142.6761-0.9184-0.56372.0491-1.02581.40260.2704-0.04240.16850.0851-0.1108-0.1977-0.525-0.1146-0.19760.25660.03380.01230.1089-0.00610.1941.4501-0.465816.1587
152.9135-1.1166-0.38771.56510.16882.87070.04520.0561-0.2472-0.39920.0868-0.64130.20390.1276-0.09310.27370.0210.06820.1517-0.04030.346312.6495-15.251.5454
161.6728-0.7615-0.18071.5861-0.29921.14880.0639-0.00810.3676-0.00780.11630.0864-0.7414-0.1339-0.19350.4930.06530.04460.21950.02010.2781-3.59836.69479.8079
173.8092.4975-0.45313.831-2.16581.65090.2808-0.3839-0.13310.3321-0.3932-0.0395-0.2581-0.07760.0310.28250.0043-0.00410.16890.00190.18136.6913-8.654925.4965
181.15840.3724-0.36150.5743-0.29110.27960.0094-0.0738-0.15130.1126-0.08840.0644-0.2443-0.04030.01990.35580.05790.0150.21370.01440.25681.4848-6.635312.3008
191.76730.5101-1.65881.1679-0.34465.32030.1134-0.01070.23610.31920.07120.2494-0.429-0.3267-0.11960.41430.16510.06170.2820.02410.3404-14.4827-3.29910.6355
202.9843-1.83851.61572.0705-1.13110.90560.13790.4735-0.2792-0.59990.0009-0.2802-0.01620.0876-0.05640.5609-0.00660.09580.3297-0.05520.28489.8077-5.7703-10.0865
214.31751.44881.971.7690.71561.50330.2824-0.2444-0.12040.24-0.0993-0.18010.07250.03430.00760.1273-0.1196-0.11030.70940.16960.227876.085430.435870.5586
221.47750.39190.5650.96540.2270.2254-0.1811-0.3711-0.15490.37130.142-0.3355-0.09070.05620.35510.11160.0901-0.19490.7940.32690.418372.938118.664774.5584
230.481-0.25110.58090.6392-0.38580.75110.042-0.5132-0.34710.2391-0.2634-0.32560.05580.6013-0.19570.2076-0.086-0.0880.64540.16090.314970.163726.606869.8694
243.67110.6687-1.92622.9378-0.92312.71460.0940.14580.2795-0.2902-0.0294-0.0987-0.27290.4336-0.1950.2058-0.0745-0.00480.27230.00860.155163.376540.344856.0105
253.20420.3453-0.74471.89010.59611.88260.0696-0.3353-0.33240.3884-0.10470.47320.00330.33480.06280.2168-0.0396-0.0130.26680.07430.236653.314325.473870.6365
260.49710.3947-0.01780.5709-0.09690.04160.2649-0.07310.16850.2426-0.18110.0133-0.45440.35930.2860.2485-0.469-0.11410.4597-0.02660.229968.255947.854462.104
274.521-5.50051.30258.5724-0.28651.43460.05940.22380.1309-0.3618-0.2798-0.1409-0.29120.23890.19680.2019-0.0677-0.01680.27330.04450.228758.572431.531346.604
280.8293-0.0501-0.28981.1942-0.0250.13820.1476-0.32660.0189-0.0799-0.2655-0.3266-0.29110.42190.06540.2673-0.122-0.02010.48740.09510.242570.205936.168860.3094
297.02853.79440.79325.63171.27830.42450.0012-0.49150.08580.6112-0.218-0.0994-0.31720.60180.07860.3921-0.1069-0.04670.49930.02530.173555.888934.77182.3304
303.66570.6575-0.39123.2639-1.07691.30690.1306-0.2171-0.17330.5623-0.17540.51490.0389-0.19440.08990.2838-0.0330.12780.2095-0.01190.351127.953214.544572.979
311.5345-0.1556-0.26651.4681-0.03671.74040.0060.0731-0.1847-0.0095-0.07440.31340.0441-0.19190.05760.1167-0.0097-0.00210.1449-0.02650.262630.306125.335762.0722
322.1824-0.2578-0.3560.9665-0.25991.72220.00430.0223-0.07820.0551-0.03010.2424-0.0357-0.15220.04110.13650.0123-0.02090.1487-0.01610.236431.932727.209761.5779
330.7919-1.1416-1.12022.16661.25772.7184-0.23910.3599-0.8156-0.0427-0.34780.22250.6425-0.22850.56210.40150.0990.00620.394-0.09940.355753.32065.333329.2834
341.1636-0.6326-1.23690.7910.20391.6353-0.21640.0791-0.4586-0.2149-0.20150.05670.59070.09910.4020.35960.10960.0490.2517-0.00270.331455.34436.123837.6947
351.91720.1663-0.43171.42850.83352.43990.03040.0988-0.0253-0.1687-0.1784-0.0048-0.14290.0080.13610.2160.05770.02250.14770.01880.193853.591323.863434.7261
360.5954-0.4339-0.89981.62910.72522.53660.04540.2758-0.1059-0.2305-0.21220.23410.0336-0.27070.11790.18090.0556-0.03980.2345-0.04470.199546.087720.479635.8528
372.0460.32252.62572.03831.42333.9482-0.21950.1123-0.0922-0.0565-0.3012-0.2160.62071.15510.16570.32140.06640.090.53850.10820.46173.004918.180637.0795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 242 )
5X-RAY DIFFRACTION5chain 'A' and (resid 243 through 291 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 23 )
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 91 )
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 182 )
9X-RAY DIFFRACTION9chain 'B' and (resid 183 through 199 )
10X-RAY DIFFRACTION10chain 'B' and (resid 200 through 290 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 23 )
12X-RAY DIFFRACTION12chain 'C' and (resid 24 through 38 )
13X-RAY DIFFRACTION13chain 'C' and (resid 39 through 91 )
14X-RAY DIFFRACTION14chain 'C' and (resid 92 through 110 )
15X-RAY DIFFRACTION15chain 'C' and (resid 111 through 139 )
16X-RAY DIFFRACTION16chain 'C' and (resid 140 through 182 )
17X-RAY DIFFRACTION17chain 'C' and (resid 183 through 199 )
18X-RAY DIFFRACTION18chain 'C' and (resid 200 through 242 )
19X-RAY DIFFRACTION19chain 'C' and (resid 243 through 269 )
20X-RAY DIFFRACTION20chain 'C' and (resid 270 through 292 )
21X-RAY DIFFRACTION21chain 'D' and (resid 3 through 20 )
22X-RAY DIFFRACTION22chain 'D' and (resid 21 through 39 )
23X-RAY DIFFRACTION23chain 'D' and (resid 40 through 91 )
24X-RAY DIFFRACTION24chain 'D' and (resid 92 through 110 )
25X-RAY DIFFRACTION25chain 'D' and (resid 111 through 139 )
26X-RAY DIFFRACTION26chain 'D' and (resid 140 through 182 )
27X-RAY DIFFRACTION27chain 'D' and (resid 183 through 198 )
28X-RAY DIFFRACTION28chain 'D' and (resid 199 through 270 )
29X-RAY DIFFRACTION29chain 'D' and (resid 271 through 291 )
30X-RAY DIFFRACTION30chain 'E' and (resid 3 through 38 )
31X-RAY DIFFRACTION31chain 'E' and (resid 39 through 182 )
32X-RAY DIFFRACTION32chain 'E' and (resid 183 through 291 )
33X-RAY DIFFRACTION33chain 'F' and (resid 3 through 23 )
34X-RAY DIFFRACTION34chain 'F' and (resid 24 through 91 )
35X-RAY DIFFRACTION35chain 'F' and (resid 92 through 182 )
36X-RAY DIFFRACTION36chain 'F' and (resid 183 through 269 )
37X-RAY DIFFRACTION37chain 'F' and (resid 270 through 292 )

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