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- PDB-4x24: Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-ade... -

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Basic information

Entry
Database: PDB / ID: 4x24
TitleCrystal structure of Vibrio cholerae 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with methylthio-DADMe-Immucillin-A
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Keywordshydrolase/hydrolase inhibitor / hydrolase / hydrolase-hydrolase inhibitor complex
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
TRIETHYLENE GLYCOL / Chem-TDI / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsCameron, S.A. / Thomas, K. / Almo, S.C. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 GM068036 United States
Citation
Journal: Biochemistry / Year: 2015
Title: Active site and remote contributions to catalysis in methylthioadenosine nucleosidases.
Authors: Thomas, K. / Cameron, S.A. / Almo, S.C. / Burgos, E.S. / Gulab, S.A. / Schramm, V.L.
#1: Journal: Nat.Chem.Biol. / Year: 2009
Title: Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing
Authors: Gutierrez, J.A. / Crowder, T. / Rinaldo-Matthis, A. / Ho, M.-C. / Almo, S.C. / Schramm, V.L.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,0695
Polymers52,3322
Non-polymers7373
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-22 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.898, 72.708, 61.621
Angle α, β, γ (deg.)90.000, 110.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase ...MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase / SRH nucleosidase


Mass: 26165.822 Da / Num. of mol.: 2 / Mutation: A113P, V153I, R158G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: mtnN, pfs, VC0395_A1957, VC395_2494 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5F5R2, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-TDI / (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL / (3R,4S)-1-[9-DEAZAADENIN-9-YL)METHYL]-3-HYDROXY-4-(METHYLTHIOMETHYL)PYRROLIDINE


Mass: 293.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N5OS
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.2 Å3/Da / Density % sol: 44.15 % / Description: rods
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: Protein (10 mg/mL); Reservoir (0.2M ammonium chloride pH 6.3 and 20% PEG 3350); Cryoprotection (20% (v/v) glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 9, 2014
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 69602 / % possible obs: 99.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.337 / Net I/av σ(I): 18.68 / Net I/σ(I): 8.9 / Num. measured all: 253993
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.5-1.533.50.6851.7833510.92496.8
1.53-1.553.50.59734450.95798
1.55-1.583.60.51334530.98398.5
1.58-1.623.60.42334450.98898.4
1.62-1.653.60.39934541.0199
1.65-1.693.60.34334480.98999.1
1.69-1.733.60.30134891.03799
1.73-1.783.60.25434681.0999.5
1.78-1.833.70.20435101.20999.5
1.83-1.893.70.17734811.29399.7
1.89-1.963.70.15135071.41999.7
1.96-2.043.70.12634751.53399.8
2.04-2.133.80.10935121.6699.9
2.13-2.243.80.10434931.67399.9
2.24-2.383.70.10535201.85399.8
2.38-2.563.60.09935022.01299.8
2.56-2.823.60.08835212.02799.7
2.82-3.233.70.06935081.62599.6
3.23-4.073.70.04935401.1799.6
4.07-503.60.03934801.11596.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREP11.2.08phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DP9

3dp9


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1856 / WRfactor Rwork: 0.1673 / FOM work R set: 0.8571 / SU B: 1.418 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0724 / SU Rfree: 0.0699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.07 / SU Rfree Cruickshank DPI: 0.0699 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 3448 5 %RANDOM
Rwork0.1687 66097 --
obs0.1696 66097 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.04 Å2 / Biso mean: 17.318 Å2 / Biso min: 8.77 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å2-0 Å2-0.24 Å2
2---0.12 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3509 0 50 360 3919
Biso mean--18.57 26.55 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193661
X-RAY DIFFRACTIONr_bond_other_d0.0010.023535
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9714979
X-RAY DIFFRACTIONr_angle_other_deg0.97238133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25926.027146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33315597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.133158
X-RAY DIFFRACTIONr_chiral_restr0.1540.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
X-RAY DIFFRACTIONr_mcbond_it0.8741.5851910
X-RAY DIFFRACTIONr_mcbond_other0.8741.5831909
X-RAY DIFFRACTIONr_mcangle_it1.4032.3742388
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 264 -
Rwork0.252 4768 -
all-5032 -
obs--97.48 %

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