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- PDB-4l6i: Methylthioadenosine phosphorylase from Schistosoma mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 4l6i
TitleMethylthioadenosine phosphorylase from Schistosoma mansoni in complex with adenine
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTRANSFERASE / phosphorylase / Nucleoside phosphorylase
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: 2.1 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 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 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)212,48214
Polymers211,5576
Non-polymers9258
Water11,422634
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)106,2417
Polymers105,7783
Non-polymers4624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-75 kcal/mol
Surface area31150 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)106,2417
Polymers105,7783
Non-polymers4624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-77 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.270, 82.550, 150.300
Angle α, β, γ (deg.)90.000, 100.610, 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-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.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 47.49 %
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: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 30, 2010 / Details: DCM
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.1→147.73 Å / Num. all: 104402 / Num. obs: 104402 / % possible obs: 91.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.121 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.215.10.5111.484973165990.511100
2.21-2.355.10.4551.460693120090.45576.5
2.35-2.515.20.2542.876789147680.254100
2.51-2.715.20.2012.958412112900.20181.9
2.71-2.975.10.1345.165066126660.134100
2.97-3.324.90.113656585114590.11399.9
3.32-3.834.60.153606977690.176.7
3.83-4.74.30.0629.53235275040.06287.3
4.7-6.644.10.053112773366930.053100
6.64-30.014.40.04811.61592936450.04896.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30.01 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8045 / SU ML: 0.24 / σ(F): 1.33 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.241 5227 5.03 %Random
Rwork0.1923 ---
all0.1947 104402 --
obs0.1947 103947 91.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.28 Å2 / Biso mean: 30.4438 Å2 / Biso min: 7.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13062 0 60 634 13756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713382
X-RAY DIFFRACTIONf_angle_d1.07818152
X-RAY DIFFRACTIONf_chiral_restr0.0662098
X-RAY DIFFRACTIONf_plane_restr0.0052324
X-RAY DIFFRACTIONf_dihedral_angle_d13.2624825
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 (%)
2.1-2.12390.29171970.225536053802100
2.1239-2.14890.25481890.218736013790100
2.1489-2.17510.271760.205635803756100
2.1751-2.20260.27321960.219535593755100
2.2026-2.23150.3471680.26213570373898
2.2315-2.26210.4815180.314538840697
2.2621-2.29440.34091450.26333167331296
2.2944-2.32860.28382070.208235703777100
2.3286-2.3650.28481880.197136113799100
2.365-2.40380.24932080.204535453753100
2.4038-2.44520.25081940.201435863780100
2.4452-2.48970.30091920.211836043796100
2.4897-2.53750.271890.207836453834100
2.5375-2.58930.25642160.201435383754100
2.5893-2.64560.29671950.217736053800100
2.6456-2.70710.3096700.22741201127134
2.7071-2.77470.23851790.20283566374599
2.7747-2.84970.2791830.195336153798100
2.8497-2.93350.25851810.21335943775100
2.9335-3.02810.29031900.216536393829100
3.0281-3.13620.26421900.210536143804100
3.1362-3.26160.25092040.210135773781100
3.2616-3.40980.25671810.203336263807100
3.4098-3.58930.26491240.20122529265370
3.5893-3.81380.20621270.18312448257568
3.8138-4.10760.19811300.16252603273371
4.1076-4.51970.17451980.140136113809100
4.5197-5.17080.16891760.142536593835100
5.1708-6.50380.18632170.165536393856100
6.5038-30.01320.21321990.17913625382497
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)
12.01840.2908-0.52713.27331.68351.81350.36750.57620.3658-0.8801-0.3176-0.2055-0.25790.2128-0.05640.26050.06340.08410.30080.04130.480215.0572-22.9714-74.4023
21.3873-0.4076-0.36630.9209-0.23441.4454-0.08420.1164-0.0302-0.14780.0201-0.30050.17920.2311-0.00730.21180.05530.09140.1245-0.05250.335212.13-29.4813-71.7923
32.2588-0.92980.41122.04660.03980.95340.12690.1549-0.3145-0.1473-0.1284-0.14270.12510.04470.0060.12790.02960.01180.0914-0.01330.18715.8466-23.9129-67.5968
41.34190.3063-0.31871.7753-0.41411.719-0.0029-0.1171-0.09540.0653-0.0653-0.02840.06270.02780.0490.1058-0.0416-0.01650.08920.00190.15993.0837-17.8275-56.75
51.3920.0752-0.10610.86850.09690.93150.076-0.07680.13880.1256-0.0623-0.1575-0.25790.1597-0.0130.152-0.0578-0.01350.11060.00120.14278.1483-7.8747-60.9789
65.00870.796-2.28216.03923.32733.3437-0.07290.44290.9297-0.3445-0.04820.4752-1.1152-0.31750.1550.37970.0777-0.01230.18320.03060.2927-4.51271.7573-69.4431
72.56460.1186-0.60131.32990.06871.2990.0055-0.0274-0.168-0.0217-0.1227-0.43840.0980.39730.11030.126-0.0069-0.02880.1264-0.05650.206214.8043-18.4806-62.7399
82-7.2522-0.78182-0.08830.0552-0.036-0.01380.00650.06840.0724-0.05230.06390.1462-0.0452-0.05730.1999-0.15460.1887-1.3212-8.1826-68.1467
90.8915-0.05010.10196.5208-2.06015.8767-0.1751-0.4185-0.62990.2236-0.071-0.24170.3540.25340.2430.2724-0.02110.08390.1865-0.00380.2457-15.1159-35.8924-29.4867
100.65570.0408-0.59620.5489-0.34470.8609-0.14190.0123-0.34030.039-0.04520.04310.3285-0.12310.1490.3051-0.13460.04210.2198-0.02030.2789-16.0336-35.2186-38.0694
111.663-0.5794-0.73481.1048-0.7071.4027-0.0057-0.05250.09090.2119-0.06570.0254-0.2522-0.08940.04740.269-0.08920.02140.15-0.01830.1619-14.0403-17.0692-34.6123
120.391-0.2265-0.76681.7165-0.40211.94690.0927-0.1944-0.05140.237-0.1424-0.1246-0.08010.14080.03340.2013-0.0806-0.02540.16730.01130.1429-5.2819-17.5795-41.0832
130.92110.3428-1.27061.5436-0.75423.166-0.0235-0.4369-0.29930.2722-0.09160.16050.0157-0.11770.090.3089-0.10130.0710.1052-0.0570.2219-17.3155-25.6358-30.6496
148.71254.4385.14868.2514-3.42929.1560.09560.34310.6697-0.17730.28330.51990.4294-0.1085-0.36970.2471-0.02180.04540.5138-0.01360.3144-1.1948-20.8085-40.496
150.693-0.3206-0.03230.8955-0.34440.17550.12930.2717-0.3028-0.1760.05510.59580.1186-0.5699-0.26790.1010.1709-0.20550.923-0.22690.4743-38.4027-12.7287-72.9495
160.4198-0.18090.57190.67720.24991.27190.08960.4136-0.2609-0.0878-0.32690.49260.1787-0.8385-0.15020.18690.0408-0.06510.5705-0.19620.3057-30.7153-17.0061-71.3483
172.2571-0.6112-1.12341.00520.34291.97660.13760.1529-0.10870.0295-0.17510.0406-0.0482-0.380800.11280.0323-0.05150.1884-0.03570.1369-17.9597-9.9625-64.7341
180.8826-0.1066-0.10840.46940.01760.7080.15870.22590.1034-0.0278-0.14550.1296-0.2956-0.3209-0.03380.23460.11570.00240.3064-0.02640.1799-24.797-1.2785-60.0874
192.0531-0.3219-0.99721.66260.65641.86120.25810.3957-0.06620.0845-0.260.12260.20710.0455-0.0540.11990.2531-0.03650.4854-0.11890.2975-39.7833-2.8775-61.8175
204.2166-2.4171.19251.3894-0.68460.33420.18630.52290.1001-0.3229-0.12950.0844-0.359-0.2973-0.00440.39060.2858-0.05410.63070.05050.1709-19.8083-3.8841-83.0085
218.3892-1.58464.69683.10362.05345.71130.09540.9363-0.0302-1.07540.2906-0.7034-0.28980.8547-0.29080.33620.04540.06650.2785-0.01720.2282-4.219-15.1707-81.5371
222.37060.67550.60442.77290.92973.12490.0895-0.3201-0.18550.2439-0.0166-0.37510.09590.4616-0.08710.1637-0.0063-0.02790.23730.04460.220947.4664-58.158-0.5023
231.0655-0.3345-0.08390.41930.46481.04760.0741-0.00610.0596-0.0324-0.0095-0.0945-0.20520.0657-0.02850.2447-0.05090.01270.11770.0020.19237.3515-44.9313-10.6809
242.85270.22640.34952.3051-0.6010.22470.03790.1204-0.0973-0.2151-0.0488-0.1406-0.25190.23060.01860.2228-0.04810.03390.1172-0.01180.169838.8864-48.9724-10.3917
252.03780.0862-0.551.13670.18871.94190.0034-0.28990.05310.07420.0407-0.0718-0.09150.1605-0.05230.2968-0.0627-0.01680.10350.0250.198939.119-46.76720.6651
262.07160.8-0.12582.0566-0.88561.11040.0421-0.1014-0.25250.3715-0.110.33440.1177-0.30620.08640.2933-0.06340.09710.3072-0.00570.34292.987-64.9534-3.4395
271.9376-0.3073-0.33171.80310.84381.6244-0.06360.17370.0687-0.1019-0.04630.1338-0.1751-0.28520.10980.23040.06320.01150.24250.01480.17035.644-50.7833-14.9454
282.26430.69850.01791.39940.25581.50730.0382-0.040.0897-0.0025-0.06680.2326-0.1415-0.31780.03920.20390.06590.0310.21310.00940.20547.9056-52.7012-10.678
295.62632.91711.42964.87713.48654.0068-0.71080.5782-0.30380.55110.3363-0.33680.7757-0.81370.3560.31530.05510.03030.37730.06060.1515.7753-48.1277-4.7646
300.7482-0.275-1.282.18390.64624.55330.02810.3449-0.2033-0.0741-0.25680.01770.6797-0.23930.2060.28390.02450.00680.235-0.0670.237730.5199-78.7486-40.1439
311.6265-0.1731-0.06391.02620.72421.48710.11110.15530.0048-0.1455-0.13420.035-0.2601-0.20240.02370.21930.07310.0130.1719-0.00370.132429.2145-62.0169-36.2902
320.428-0.0083-0.44382.15910.24151.47960.110.2762-0.0279-0.16-0.23080.3705-0.2894-0.48520.08930.23880.1003-0.010.296-0.04530.179819.884-57.5952-32.024
331.96550.1466-0.38841.41480.71932.98110.06450.5532-0.2519-0.1972-0.076-0.065-0.0617-0.02960.01710.22840.08950.03340.12840.00620.172932.2509-66.1698-41.9683
344.10311.95752.97098.72413.85182.9119-0.0326-0.32360.30160.36660.379-0.82940.70120.0774-0.33520.36440.0658-0.03690.3512-0.14350.163515.9387-60.7209-32.7366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 139 )
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 230 )
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 242 )
7X-RAY DIFFRACTION7chain 'A' and (resid 243 through 291 )
8X-RAY DIFFRACTION8chain 'A' and (resid 301 through 301 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 23 )
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 90 )
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 182 )
12X-RAY DIFFRACTION12chain 'B' and (resid 183 through 242 )
13X-RAY DIFFRACTION13chain 'B' and (resid 243 through 290 )
14X-RAY DIFFRACTION14chain 'B' and (resid 301 through 301 )
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 26 )
16X-RAY DIFFRACTION16chain 'C' and (resid 27 through 89 )
17X-RAY DIFFRACTION17chain 'C' and (resid 90 through 139 )
18X-RAY DIFFRACTION18chain 'C' and (resid 140 through 229 )
19X-RAY DIFFRACTION19chain 'C' and (resid 243 through 269 )
20X-RAY DIFFRACTION20chain 'C' and (resid 270 through 287 )
21X-RAY DIFFRACTION21chain 'C' and (resid 288 through 292 )
22X-RAY DIFFRACTION22chain 'F' and (resid 3 through 78 )
23X-RAY DIFFRACTION23chain 'F' and (resid 79 through 199 )
24X-RAY DIFFRACTION24chain 'F' and (resid 200 through 242 )
25X-RAY DIFFRACTION25chain 'F' and (resid 243 through 299 )
26X-RAY DIFFRACTION26chain 'D' and (resid 4 through 90 )
27X-RAY DIFFRACTION27chain 'D' and (resid 91 through 182 )
28X-RAY DIFFRACTION28chain 'D' and (resid 183 through 292 )
29X-RAY DIFFRACTION29chain 'D' and (resid 301 through 301 )
30X-RAY DIFFRACTION30chain 'E' and (resid 3 through 53 )
31X-RAY DIFFRACTION31chain 'E' and (resid 54 through 182 )
32X-RAY DIFFRACTION32chain 'E' and (resid 183 through 242 )
33X-RAY DIFFRACTION33chain 'E' and (resid 243 through 290 )
34X-RAY DIFFRACTION34chain 'E' and (resid 301 through 301 )

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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