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- PDB-4f1w: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocystein... -

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Basic information

Entry
Database: PDB / ID: 4f1w
TitleCrystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with Adenine
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / 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
Function / homologyNucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ADENINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / :
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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 Adenine
Authors: Haapalainen, A.M. / Thomas, K. / Tyler, P.C. / Evans, G.B. / Almo, S.C. / Schramm, V.L.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)54,35717
Polymers52,6482
Non-polymers1,70915
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint3 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.050, 68.120, 89.660
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 , 6 types, 401 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0M (NH4)2HPO4, 0.1M Imidazole, pH 8.0, 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: Aug 25, 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: 1.36→54.24 Å / Num. all: 87459 / Num. obs: 87459 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 12.9
Reflection shellResolution: 1.36→1.43 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 12605 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0025refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3O4V

3o4v


Resolution: 1.36→41.95 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.47 / SU ML: 0.027 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14597 4379 5 %RANDOM
Rwork0.11286 ---
all0.11455 87381 --
obs0.11455 83002 99.94 %-
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: 15.932 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.36→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 114 386 3945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193851
X-RAY DIFFRACTIONr_bond_other_d0.0020.023866
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9845239
X-RAY DIFFRACTIONr_angle_other_deg0.8123.0018938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5845542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.425.096157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7415664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2721519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02820
X-RAY DIFFRACTIONr_rigid_bond_restr2.18637717
X-RAY DIFFRACTIONr_sphericity_free38.3735100
X-RAY DIFFRACTIONr_sphericity_bonded10.40157930
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 317 -
Rwork0.245 6052 -
obs-6052 99.7 %

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