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- PDB-1jys: Crystal Structure of E. coli MTA/AdoHcy Nucleosidase -

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Basic information

Entry
Database: PDB / ID: 1jys
TitleCrystal Structure of E. coli MTA/AdoHcy Nucleosidase
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
ADENINE / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsLee, J.E. / Cornell, K.A. / Riscoe, M.K. / Howell, P.L.
CitationJournal: Structure / Year: 2001
Title: Structure of E. coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase reveals similarity to the purine nucleoside phosphorylases.
Authors: Lee, J.E. / Cornell, K.A. / Riscoe, M.K. / Howell, P.L.
History
DepositionSep 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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)51,2474
Polymers50,9762
Non-polymers2702
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-15 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.080, 133.030, 70.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MTA/SAH nucleosidase / MTA/AdoHcy Nucleosidase / S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE


Mass: 25488.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pfs / Plasmid: pPROEX HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P24247, UniProt: P0AF12*PLUS, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: sodium citrate, CHES, CHAPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.7 Msodium citrate1drop
3100 mMCHES1droppH8.5
40.8 mMCHAPS detergent1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X8C10.97913, 0.97898, 0.96379
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 17, 2000
RIGAKU RAXIS IV2IMAGE PLATEOct 22, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979131
20.978981
30.963791
41.54181
ReflectionResolution: 1.9→50 Å / Num. all: 210105 / Num. obs: 205182 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.215 / % possible all: 87.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. obs: 38710 / Num. measured all: 205182
Reflection shell
*PLUS
% possible obs: 95.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→50 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1727 4.6 %Random
Rwork0.217 ---
all-37732 --
obs-37547 97.1 %-
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--7.02 Å20 Å2
3----6.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 20 215 3549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 182 3.2 %
Rwork0.289 5536 -
obs-5536 90 %
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. reflection obs: 37764 / Num. reflection Rfree: 1888 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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