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- PDB-4l0m: Crystal structure of a putative 5'-methylthioadenosine/S-adenosyl... -

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Basic information

Entry
Database: PDB / ID: 4l0m
TitleCrystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Borrelia burgdorferi B31 bound to Adenine (Target NYSGRC-029268 )
Componentsputative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / Borrelia burgdorferi B31 / 5'-methylthioadenosine nucleosidase / Adenine / BB_0375 / pfs gene product / Structural genomics / NYSGRC / New York Structural Genomics Research Consortium / PSI-Biology
Function / homology
Function and homology information


adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside catabolic process / L-methionine salvage from methylthioadenosine
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
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Borrelia burgdorferi B31 bound to Adenine (Target NYSGRC-029268 )
Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Eromenok, G. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Himmel, D.M. / Hillerich, B. / ...Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Eromenok, G. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Himmel, D.M. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Morisco, L.L. / Sojitra, S.S. / Wasserman, S.R. / Haapalainen, A. / Suarez, J. / Schramm, V.L. / Almo, S.C.
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,5502
Polymers29,4151
Non-polymers1351
Water2,054114
1
A: putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)59,1004
Polymers58,8302
Non-polymers2702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4520 Å2
ΔGint-12 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.083, 48.083, 241.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

21A-476-

HOH

Detailsprobable dimer

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Components

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


Mass: 29415.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein expressed as N-terminal Hexa-histidine tag with TEV protease site
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: BB_0375, BB_0375 pfs gene product, pfs / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL
References: UniProt: O50162, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-ADE / ADENINE / Adenine


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


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG2 #27: 0.2 M Ammonium Acetate, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350 ); Cryoprotection (33% Ethylene ...Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG2 #27: 0.2 M Ammonium Acetate, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350 ); Cryoprotection (33% Ethylene glycol), Sitting Drop, Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 14, 2013 / Details: MIRRORS
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.7→37.63 Å / Num. obs: 32546 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.9 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 28.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 26.8 % / Rmerge(I) obs: 2.21 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1656 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
XDSdata reduction
Aimlessdata scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→34.12 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.461 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 1641 5.1 %RANDOM
Rwork0.2266 ---
obs0.2286 32426 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.18 Å2 / Biso mean: 36.0311 Å2 / Biso min: 14.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2--1.81 Å2-0 Å2
3----3.62 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 10 114 1996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191968
X-RAY DIFFRACTIONr_bond_other_d0.0010.022011
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9872664
X-RAY DIFFRACTIONr_angle_other_deg0.81934661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17727.10883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34115396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.643152
X-RAY DIFFRACTIONr_chiral_restr0.0980.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
LS refinement shellResolution: 1.701→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 123 -
Rwork0.371 2175 -
all-2298 -
obs-2175 99.39 %

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