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- PDB-4f3k: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocystein... -

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Basic information

Entry
Database: PDB / ID: 4f3k
TitleCrystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with homocysteine-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 / hydrolase activity / acting on glycosyl bonds / hydrolase-hydrolase inhibitor complex
Function / homologyNucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-HCE / :
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 homocysteine-DADMe-Immucillin-A
Authors: Haapalainen, A.M. / Thomas, K. / Tyler, P.C. / Evans, G.B. / Almo, S.C. / Schramm, V.L.
History
DepositionMay 9, 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

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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)53,5336
Polymers52,6482
Non-polymers8854
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-17 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.490, 70.490, 122.830
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 (bacteria)
Strain: SCSA50 / Gene: EMBL EFZ04802.1, mtnN, pfs, SCA50_0219 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: E8NLP5, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-HCE / {(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-hydroxypyrrolidin-3-yl}-L-methionine / homocysteine-DADMe-Immucillin-A


Mass: 380.465 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N6O3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG 20000, 0.1M MES, 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: Feb 9, 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: 1.85→61.41 Å / Num. all: 39679 / Num. obs: 39679 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.153 / Rsym value: 0.153
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5700 / Rsym value: 0.865 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0025refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→39.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.527 / SU ML: 0.103 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21477 1991 5 %RANDOM
Rwork0.17755 ---
all0.1795 39608 --
obs0.1795 37617 99.72 %-
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: 22.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--2.42 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 0 60 247 3711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193560
X-RAY DIFFRACTIONr_bond_other_d0.0040.023506
X-RAY DIFFRACTIONr_angle_refined_deg1.381.984840
X-RAY DIFFRACTIONr_angle_other_deg1.1123.0078063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0095476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35525.493142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66515594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3751514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02753
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 151 -
Rwork0.254 2723 -
obs-2874 99.27 %

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