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- PDB-3o4v: Crystal structure of E. coli MTA/SAH nucleosidase in complex with... -

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Basic information

Entry
Database: PDB / ID: 3o4v
TitleCrystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA
ComponentsMTA/SAH nucleosidase
KeywordsHYDROLASE / mixed alpha/beta dimer
Function / homology
Function and homology information


toxic metabolite repair / purine deoxyribonucleoside catabolic process / L-methionine salvage from S-adenosylmethionine / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from methylthioadenosine / protein homodimerization activity / identical protein binding / cytosol
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-4CT / ISOPROPYL ALCOHOL / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSiu, K.K.W. / Howell, P.L.
CitationJournal: To be Published
Title: Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA
Authors: Siu, K.K.W. / Howell, P.L.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: MTA/SAH nucleosidase
B: MTA/SAH nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4339
Polymers49,2242
Non-polymers1,2087
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-24 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.600, 69.090, 128.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MTA/SAH nucleosidase


Mass: 24612.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mtn, pfs / Plasmid: pPROEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: D3QWG1, UniProt: P0AF12*PLUS, adenosylhomocysteine nucleosidase, methylthioadenosine nucleosidase
#2: Chemical ChemComp-4CT / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol


Mass: 389.902 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20ClN5OS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 60 mM Sodium acetate, pH 4.6, 35% (v/v) isopropanol, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2005 / Details: MIRRORS
RadiationMonochromator: CONFOCAL MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.75→32.93 Å / Num. obs: 46533 / % possible obs: 98.8 % / Redundancy: 12.31 % / Rmerge(I) obs: 0.049 / Χ2: 0.93 / Net I/σ(I): 29.5 / Scaling rejects: 30157
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.75-1.8110.30.2847.85735444081.2495.1
1.81-1.8911.440.19610.75801244941.0696.6
1.89-1.9712.390.14913.75832145710.9898.1
1.97-2.0712.440.11416.85893646000.9499.1
2.07-2.212.590.08521.75983146140.9399
2.2-2.3712.70.0725.36056446450.999.4
2.37-2.6112.810.0629.86173747010.8999.8
2.61-2.9912.880.04637.16205247170.87100
2.99-3.7712.930.03149.36297947870.82100
3.77-32.9312.470.02270.56333649960.82100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.4Ldata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→21.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 4679 10.1 %RANDOM
Rwork0.1523 ---
obs0.1565 46449 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.83 Å2 / Biso mean: 14.5508 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.75→21.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 80 339 3854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223701
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.9855051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76925.828151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71415608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8411512
X-RAY DIFFRACTIONr_chiral_restr0.2030.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212785
X-RAY DIFFRACTIONr_mcbond_it1.2411.52382
X-RAY DIFFRACTIONr_mcangle_it223824
X-RAY DIFFRACTIONr_scbond_it3.28631319
X-RAY DIFFRACTIONr_scangle_it5.3834.51208
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 308 -
Rwork0.442 3001 -
all-3309 -
obs--95.58 %

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