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- PDB-4f2w: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocystein... -

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Basic information

Entry
Database: PDB / ID: 4f2w
TitleCrystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with methyl-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-TDI / :
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Choleraesuis str. SCSA50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 methyl-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 / 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: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,67812
Polymers52,6482
Non-polymers1,03010
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-31 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.410, 82.540, 93.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 str. SCSA50 (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
#2: Chemical ChemComp-TDI / (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL / (3R,4S)-1-[9-DEAZAADENIN-9-YL)METHYL]-3-HYDROXY-4-(METHYLTHIOMETHYL)PYRROLIDINE


Mass: 293.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N5OS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 35% 2-methyl-2,4-pentanediol, 0.2M sodium chloride, 0.1M Tris, pH 7.0, 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: Feb 9, 2011
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: 2→61.77 Å / Num. all: 36435 / Num. obs: 36435 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.196 / Rsym value: 0.196 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.347 / % possible all: 96.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0025refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.18 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.538 / SU ML: 0.099 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21597 1817 5 %RANDOM
Rwork0.17717 ---
obs0.17911 34563 98.77 %-
all-36380 --
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: 16.933 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 66 271 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193612
X-RAY DIFFRACTIONr_bond_other_d0.0040.023565
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9784898
X-RAY DIFFRACTIONr_angle_other_deg1.0343.0068189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14325.245143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9115601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6341515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02768
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 127 -
Rwork0.207 2439 -
obs--96.1 %

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