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

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Basic information

Entry
Database: PDB / ID: 4wkc
TitleCrystal structure of Escherichia coli 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with butylthio-DADMe-Immucillin-A
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Keywordshydrolase/hydrolase inhibitor / hydrolase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


purine deoxyribonucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine
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-BIG / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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: Biochemistry / Year: 2015
Title: Active site and remote contributions to catalysis in methylthioadenosine nucleosidases.
Authors: Thomas, K. / Cameron, S.A. / Almo, S.C. / Burgos, E.S. / Gulab, S.A. / Schramm, V.L.
#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
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,5883
Polymers26,0591
Non-polymers5302
Water3,027168
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)53,1776
Polymers52,1172
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area3420 Å2
ΔGint-16 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.396, 91.386, 70.640
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-402-

HOH

21A-448-

HOH

31A-463-

HOH

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Components

#1: Protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase ...MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / 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 O139:H28 (bacteria) / Strain: E24377A / ETEC / Gene: mtnN, EcE24377A_0164 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A7ZHQ1, adenosylhomocysteine nucleosidase
#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.: 1 / Source method: obtained synthetically / Formula: C16H25N5OS
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 44.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (10 mg/mL); Reservoir (0.2M ammonium acetate, 0.1M BIS-TRIS pH5.5 and 25% PEG 3350); Cryoprotection (20% (v/v) glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2014
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 28677 / % possible obs: 99.9 % / Redundancy: 11.5 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.33 / Net I/av σ(I): 32.918 / Net I/σ(I): 11.2 / Num. measured all: 330430
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.64-1.679.60.5374.1913941.03198.3
1.67-1.7110.4714281.093100
1.7-1.73110.42713891.089100
1.73-1.7711.10.36814351.098100
1.77-1.8111.30.31214061.179100
1.81-1.8511.30.27614011.214100
1.85-1.8911.50.22414331.292100
1.89-1.9411.60.19814321.35100
1.94-211.80.16414221.437100
2-2.0712.10.14214241.48100
2.07-2.1412.10.11914271.525100
2.14-2.2312.10.10214291.571100
2.23-2.3312.10.09614201.471100
2.33-2.4512.10.08714251.495100
2.45-2.612.10.08114411.415100
2.6-2.811.90.07614351.551100
2.8-3.0911.80.07414571.468100
3.09-3.5311.60.06314561.368100
3.53-4.4511.20.0514801.155100
4.45-50110.05315431.14599.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y6Q

1y6q


Resolution: 1.64→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1838 / WRfactor Rwork: 0.158 / FOM work R set: 0.8886 / SU B: 1.476 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0837 / SU Rfree: 0.0825 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.083 / SU Rfree Cruickshank DPI: 0.0825 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 1349 4.7 %RANDOM
Rwork0.1593 27298 --
obs0.1606 27298 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.03 Å2 / Biso mean: 18.061 Å2 / Biso min: 9.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å20 Å2
2--0.17 Å2-0 Å2
3---0.57 Å2
Refinement stepCycle: final / Resolution: 1.64→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 36 168 1912
Biso mean--17.87 27.37 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191803
X-RAY DIFFRACTIONr_bond_other_d0.0010.021775
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.982450
X-RAY DIFFRACTIONr_angle_other_deg0.75634089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75225.69472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98915296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.456156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022073
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02387
X-RAY DIFFRACTIONr_mcbond_it0.9561.609941
X-RAY DIFFRACTIONr_mcbond_other0.951.606940
X-RAY DIFFRACTIONr_mcangle_it1.5362.4081178
LS refinement shellResolution: 1.64→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 85 -
Rwork0.189 1976 -
all-2061 -
obs--99.28 %

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