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- PDB-3mms: Crystal structure of Streptococcus pneumoniae MTA/SAH nucleosidas... -

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Basic information

Entry
Database: PDB / ID: 3mms
TitleCrystal structure of Streptococcus pneumoniae MTA/SAH nucleosidase in complex with 8-aminoadenine
Components5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / mixed alpha/beta hydrolase
Function / homology
Function and homology information


adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / 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
9H-purine-6,8-diamine / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSiu, K.K.W. / Lee, J.E. / Horvatin-Mrakovcic, C. / Howell, P.L.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Streptococcus pneumoniae MTA/SAH nucleosidase in complex with 8-aminoadenine
Authors: Siu, K.K.W. / Lee, J.E. / Horvatin-Mrakovcic, C. / Howell, P.L.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0444
Polymers24,6521
Non-polymers3923
Water3,837213
1
A: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
hetero molecules

A: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0898
Polymers49,3042
Non-polymers7856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation27_455-x-1/2,y,-z1
Buried area3680 Å2
ΔGint-33 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.720, 145.720, 145.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

21A-446-

HOH

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Components

#1: Protein 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase


Mass: 24651.988 Da / Num. of mol.: 1 / Mutation: T23A, A39V, D64V, T184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC 6303 / Gene: mtnN, pfs, SPP_0997, spr0894 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q8DQ16, UniProt: A0A0H2UPP7*PLUS, methylthioadenosine nucleosidase
#2: Chemical ChemComp-Q88 / 9H-purine-6,8-diamine / 8-aminoadenine


Mass: 150.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.26 M sodium citrate, 90 mM sodium HEPES, pH 7.5, 10 % (v/v) glycerol, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 16, 2002
RadiationMonochromator: CONFOCAL MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→32.58 Å / Num. obs: 34861 / % possible obs: 99.7 % / Redundancy: 17.28 % / Rmerge(I) obs: 0.041 / Χ2: 1.21 / Net I/σ(I): 13.6 / Scaling rejects: 12528
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.8 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRMethod translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→35 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.199 1722 4.9 %
Rwork0.182 --
obs-34787 99.5 %
Solvent computationBsol: 46.078 Å2
Displacement parametersBiso max: 55.21 Å2 / Biso mean: 16.497 Å2 / Biso min: 4.57 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 28 213 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.7361.5
X-RAY DIFFRACTIONc_scbond_it1.3832
X-RAY DIFFRACTIONc_mcangle_it1.1892
X-RAY DIFFRACTIONc_scangle_it2.0722.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3qx88.param

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