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- PDB-4f2p: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocystein... -

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Basic information

Entry
Database: PDB / ID: 4f2p
TitleCrystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with diEtglycol-thio-DADMe-Immucillin-A
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE/HYDROLASE inhibitor / L-methionine biosynthetic process from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / acting on glycosyl bonds / HYDROLASE-HYDROLASE inhibitor complex
Function / homologyNucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-2EL / ACETATE ION / :
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsHaapalainen, A.M. / Thomas, K. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
CitationJournal: Structure / Year: 2013
Title: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with diEtglycol-thio-DADMe-Immucillin-A
Authors: Haapalainen, A.M. / Thomas, K. / Tyler, P.C. / Evans, G.B. / Almo, S.C. / Schramm, V.L.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7809
Polymers52,6482
Non-polymers1,1327
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-25 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.410, 70.140, 122.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTA/SAH nucleosidase / MTAN / 5'-methylthioadenosine nucleosidase / S-adenosylhomocysteine nucleosidase


Mass: 26324.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Choleraesuis (bacteria)
Strain: SCSA50 / Gene: EMBL EFZ04802.1, mtnN, pfs, SCA50_0219, SCH_0207 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: E8NLP5, adenosylhomocysteine nucleosidase

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Non-polymers , 5 types, 345 molecules

#2: Chemical ChemComp-2EL / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[2-(2-hydroxyethoxy)ethyl]sulfanyl}methyl)pyrrolidin-3- ol / DIETGLYCOL-THIO-DADME-IMMUCILLIN-A


Mass: 367.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O3S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 27% PEG 3350, 0.2M sodium acetate, 0.1M HEPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Mar 15, 2012
Details: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.64→61.25 Å / Num. all: 55300 / Num. obs: 55300 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 10.9
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7822 / % possible all: 97.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0025refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→39.85 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.055 / SU ML: 0.068 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 2811 5.1 %RANDOM
Rwork0.16329 ---
all0.16487 55244 --
obs0.16487 52433 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--2.52 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 1.64→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 76 338 3895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193726
X-RAY DIFFRACTIONr_bond_other_d0.0050.023685
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9895069
X-RAY DIFFRACTIONr_angle_other_deg1.3153.018482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93125.203148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7315618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6541516
X-RAY DIFFRACTIONr_chiral_restr0.080.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 218 -
Rwork0.289 3729 -
obs-3947 96.43 %

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