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

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Basic information

Entry
Database: PDB / ID: 4wkb
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
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: 1.37 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
DepositionOct 2, 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 ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
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)53,0394
Polymers52,4522
Non-polymers5872
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-23 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.192, 72.002, 61.648
Angle α, β, γ (deg.)90.000, 110.320, 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: 26225.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.11 Å3/Da / Density % sol: 41.72 % / Description: Block
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Protein (10 mg/mL); Reservoir (0.1M di-ammonium hydrogen citrate and 15% PEG 3350); Cryoprotection (20% (v/v) glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2014
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 85031 / % possible obs: 93 % / Redundancy: 3.9 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.291 / Net I/av σ(I): 27.33 / Net I/σ(I): 16.2 / Num. measured all: 330001
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.37-1.393.50.226.7745101.14799.1
1.39-1.423.70.19444761.11699.2
1.42-1.453.70.18345431.1299.2
1.45-1.483.70.14545341.28899.4
1.48-1.513.80.13145211.3199.5
1.51-1.543.80.11245251.33599.6
1.54-1.583.90.09845571.37199.7
1.58-1.6240.08745661.45899.8
1.62-1.6740.08145251.4999.9
1.67-1.734.10.07245571.505100
1.73-1.794.10.06445911.46499.9
1.79-1.864.10.05845181.56699.9
1.86-1.943.50.05427531.39859.9
1.94-2.054.10.0545581.44899.9
2.05-2.174.10.04945511.24799.9
2.17-2.343.80.04927911.10360.9
2.34-2.5840.04945821.0799.7
2.58-2.9540.04145851.04799.5
2.95-3.723.80.03635351.10477
3.72-503.80.03432530.9969.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3dp9


Resolution: 1.37→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1978 / WRfactor Rwork: 0.1739 / FOM work R set: 0.8889 / SU B: 0.81 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0587 / SU Rfree: 0.0584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.058 / SU Rfree Cruickshank DPI: 0.0584 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.183 4126 4.9 %RANDOM
Rwork0.1645 80872 --
obs0.1654 80872 92.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 40.33 Å2 / Biso mean: 13.758 Å2 / Biso min: 6.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å2-0.69 Å2
2---0.34 Å20 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.37→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3535 0 40 431 4006
Biso mean--9.04 24.29 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193686
X-RAY DIFFRACTIONr_bond_other_d0.0010.023590
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9685011
X-RAY DIFFRACTIONr_angle_other_deg0.75538260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9595488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68425.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67515619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5991510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02804
X-RAY DIFFRACTIONr_mcbond_it0.7241.2341910
X-RAY DIFFRACTIONr_mcbond_other0.7241.2341909
X-RAY DIFFRACTIONr_mcangle_it1.1991.8512388
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 317 -
Rwork0.208 6327 -
all-6644 -
obs--99 %

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