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- PDB-4yml: Crystal structure of Escherichia coli 5'-methylthioadenosine/S-ad... -

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Basic information

Entry
Database: PDB / ID: 4yml
TitleCrystal structure of Escherichia coli 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3S,4R)-methylthio-DADMe-Immucillin-A
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHydrolase/Hydrolase Inhibitor / hydrolase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


toxic metabolite repair / purine deoxyribonucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
MTA/SAH nucleosidase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4F0 / PHOSPHATE ION / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsCameron, S.A. / Thomas, K. / Almo, S.C. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 GM068036 United States
Citation
Journal: Bioorg.Med.Chem. / Year: 2015
Title: Tight binding enantiomers of pre-clinical drug candidates.
Authors: Evans, G.B. / Cameron, S.A. / Luxenburger, A. / Guan, R. / Suarez, J. / Thomas, K. / Schramm, V.L. / Tyler, P.C.
#1: Journal: J. Biol. Chem. / Year: 2005
Title: Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.
Authors: Lee, J.E. / Singh, V. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Cornell, K.A. / Riscoe, M.K. / Schramm, V.L. / Howell, P.L.
History
DepositionMar 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4473
Polymers26,0591
Non-polymers3882
Water2,342130
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules

A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8946
Polymers52,1172
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area3250 Å2
ΔGint-36 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.950, 91.950, 69.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-432-

HOH

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Components

#1: Protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / P46 / S-adenosylhomocysteine ...MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / P46 / S-adenosylhomocysteine nucleosidase / SRH nucleosidase


Mass: 26058.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: mtnN, mtn, pfs, yadA, b0159, JW0155 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AF12, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-4F0 / (3S,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(methylsulfanyl)methyl]pyrrolidin-3-ol


Mass: 293.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N5OS
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.21 Å3/Da / Density % sol: 44.3 % / Description: Rod
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein (10 mg/mL); Reservoir (0.1 M BIS-TRIS pH 7.0 and 2.4 M sodium malonate)

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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: 1.75→25 Å / Num. obs: 19032 / % possible obs: 84.1 % / Observed criterion σ(I): -3 / Redundancy: 3.74 % / Biso Wilson estimate: 28.508 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.073 / Χ2: 1.002 / Net I/σ(I): 14.08 / Num. measured all: 142408
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.75-1.790.7920.6692.4411985329632220.78197.8
1.79-1.840.8860.4693.412626330232970.54699.8
1.84-1.890.8880.4613.57639318421570.54467.7
1.89-1.950.7910.8081.98227730918590.97727.8
1.95-2.020.9720.2096.4810286297727350.24491.9
2.02-2.090.9710.2066.676224289517660.24361
2.09-2.170.9860.1449.5110730280227910.16899.6
2.17-2.250.9880.11810.897369265619680.13874.1
2.25-2.350.990.112.438482256222510.11787.9
2.35-2.470.9940.07915.099606247224700.09299.9
2.47-2.60.9950.06917.169082233923370.0899.9
2.6-2.760.9950.06218.356229222317010.07376.5
2.76-2.950.9960.05222.378054207120690.0699.9
2.95-3.190.9970.04624.957456192919260.05399.8
3.19-3.490.9970.04326.785371180414520.0580.5
3.49-3.910.9970.04129.084160159311580.04872.7
3.91-4.510.9980.03331.675109142913360.03893.5
4.51-5.520.9980.0333.574631118811860.03599.8
5.52-7.810.9980.03332.1535719229160.03999.3
7.810.9970.02932.6815215204500.03586.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREP11.2.08phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y6Q

1y6q


Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1912 / WRfactor Rwork: 0.1648 / FOM work R set: 0.8466 / SU B: 2.533 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1289 / SU Rfree: 0.1163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 1002 5 %RANDOM
Rwork0.1715 ---
obs0.1728 19032 84.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.13 Å2 / Biso mean: 23.758 Å2 / Biso min: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 25 130 1848
Biso mean--25.39 31.39 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191750
X-RAY DIFFRACTIONr_bond_other_d0.0010.021707
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9812379
X-RAY DIFFRACTIONr_angle_other_deg0.76333920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8855234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47425.58868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29415284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.588156
X-RAY DIFFRACTIONr_chiral_restr0.070.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
X-RAY DIFFRACTIONr_mcbond_it1.1942.177927
X-RAY DIFFRACTIONr_mcbond_other1.1852.174926
X-RAY DIFFRACTIONr_mcangle_it1.8143.2561158
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 85 -
Rwork0.24 1620 -
all-1705 -
obs--99.94 %

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