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- PDB-4pr3: Crystal structure of Brucella melitensis 5'-methylthioadenosine/S... -

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Basic information

Entry
Database: PDB / ID: 4pr3
TitleCrystal structure of Brucella melitensis 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Components5'-methylthioadenosine nucleosidase / s-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / mixed alpha/beta
Function / homology
Function and homology information


methylthioadenosine nucleosidase / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside metabolic process
Similarity search - Function
5-methylthioadenosine/S-adenosylhomocysteine nucleosidase, putative / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / PHOSPHATE ION / 5'-methylthioadenosine nucleosidase / s-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesBrucella melitensis bv. 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.606 Å
AuthorsZhang, X.C. / Kang, X.S. / Zhao, Y. / Jiang, D.H. / Li, X.M. / Chen, Z.L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure and biochemical studies of Brucella melitensis 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Authors: Kang, X.S. / Zhao, Y. / Jiang, D.H. / Li, X.M. / Wang, X.P. / Wu, Y. / Chen, Z.L. / Zhang, X.C.
History
DepositionMar 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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 nucleosidase / s-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine nucleosidase / s-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9637
Polymers50,4112
Non-polymers5525
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-32 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.326, 97.326, 175.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 25205.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis bv. 1 (bacteria) / Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEII0888 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8YBL1, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20%(w/v) PEG-1000, 0.1M phosphate-citrate (pH 4.2), 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 4, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 15654 / Num. obs: 15654 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 40.66 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.606→37.377 Å / FOM work R set: 0.8162 / SU ML: 0.3 / σ(F): 0 / Phase error: 24.41 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 1528 9.94 %RANDOM
Rwork0.2222 ---
obs0.2262 15368 98.22 %-
all-15368 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.38 Å2 / Biso mean: 21.55 Å2 / Biso min: 4.69 Å2
Refinement stepCycle: LAST / Resolution: 2.606→37.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 36 70 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043000
X-RAY DIFFRACTIONf_angle_d0.9874069
X-RAY DIFFRACTIONf_chiral_restr0.084485
X-RAY DIFFRACTIONf_plane_restr0.004521
X-RAY DIFFRACTIONf_dihedral_angle_d12.8051072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6064-2.69050.3511210.26821162128393
2.6905-2.78660.34111320.24541210134296
2.7866-2.89820.29761350.22461207134298
2.8982-3.030.28641380.22771226136498
3.03-3.18970.26841350.22261230136598
3.1897-3.38940.23171380.21671243138199
3.3894-3.65090.27331390.2091258139799
3.6509-4.01790.23471430.195612741417100
4.0179-4.59840.24791440.193112961440100
4.5984-5.79010.23721460.227913131459100
5.7901-37.38110.26771570.253914211578100

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