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- PDB-5cce: Joint X-ray/neutron structure of wild type MTAN complexed with SR... -

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Basic information

Entry
Database: PDB / ID: 5cce
TitleJoint X-ray/neutron structure of wild type MTAN complexed with SRH and adenine
Components5'-Methylthioadenosine Nucleosidase
KeywordsHYDROLASE / Helicobacter pylori / binding sites / s-adenosylhomocysteine / n-glycosyl neutron / deuterium / nucleosidase
Function / homology
Function and homology information


aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside catabolic process / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process / 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
S-ribosylhomocysteine / ADENINE / : / DEUTERATED WATER / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBanco, M.T. / Kovalevsky, A.Y. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Aeronautic Space Administration (NASA, United States)N-123528-01 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states.
Authors: Banco, M.T. / Mishra, V. / Ostermann, A. / Schrader, T.E. / Evans, G.B. / Kovalevsky, A. / Ronning, D.R.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-Methylthioadenosine Nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3804
Polymers24,9761
Non-polymers4043
Water1,26170
1
A: 5'-Methylthioadenosine Nucleosidase
hetero molecules

A: 5'-Methylthioadenosine Nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7608
Polymers49,9522
Non-polymers8096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area3450 Å2
ΔGint-21 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.189, 83.189, 67.633
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-470-

DOD

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Components

#1: Protein 5'-Methylthioadenosine Nucleosidase / Aminofutalosine nucleosidase / Aminodeoxyfutalosine nucleosidase / 5'-methylthioadenosine/S- ...Aminofutalosine nucleosidase / Aminodeoxyfutalosine nucleosidase / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTAN / 6-amino-6-deoxyfutalosine N-ribosylhydrolase


Mass: 24975.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: mtnN, mtn, jhp_0082 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ZMY2, aminodeoxyfutalosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Sugar ChemComp-2WP / S-ribosylhomocysteine / (2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid


Type: D-saccharide, alpha linking / Mass: 267.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17NO6S
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical ChemComp-D8U / deuterium(1+)


Mass: 2.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: D
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
Method
NEUTRON DIFFRACTION
X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG550 MME, 50 mM magnesium chloride hexahydrate, 100 mM HEPES, pH 7

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12961
22961
Diffraction source
SourceTypeIDWavelength (Å)
NUCLEAR REACTOROTHER12.66
ROTATING ANODERIGAKU21.54
Detector
TypeIDDetectorDate
CUSTOM-MADE1IMAGE PLATEJan 15, 2013
RIGAKU RAXIS IV++2IMAGE PLATEJan 15, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.661
21.541
Reflection

Entry-ID: 5CCE

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.5-50939397.13.90.1111.5
1.82-4023011944.40.026243.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.593.20.6811.7194.9
1.82-1.894.50.4962.9290.8

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata processing
SCALEPACKdata scaling
HKL-3000data processing
Cootmodel building
Omodel building
nCNS1.0.0refinement
Refinement

Biso max: 117.37 Å2 / Biso mean: 31.49 Å2 / Biso min: 0 Å2 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: PDB entry 3NM5

3nm5

/ Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDBsol (Å2)ksol (e/Å3)
2.5-31.79neutron diffraction0.3760.020.3433567503965578594.581.4129.95530.657036
1.82-31.79x-ray diffraction0.2570.0080.2539971925624544202534.982.537.08550.361679
Refine analyze
Refine-ID#notag 0
neutron diffraction
FreeObs
Luzzati coordinate error0.480.4
Luzzati d res low-5
Luzzati sigma a0.460.34
x-ray diffraction
FreeObs
Luzzati coordinate error0.290.29
Luzzati d res low-5
Luzzati sigma a0.30.29
Refinement stepCycle: LAST / Resolution: 2.5→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 27 70 1852
Refine LS restraints
Refine-IDTypeDev ideal
neutron diffractionx_bond_d0.129
neutron diffractionx_angle_deg4.4
neutron diffractionx_torsion_deg19.7
neutron diffractionx_torsion_impr_deg14.6
x-ray diffractionx_bond_d0.129
x-ray diffractionx_angle_deg4.4
x-ray diffractionx_torsion_deg19.7
x-ray diffractionx_torsion_impr_deg14.6
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.610.389334.80.328659neutron diffraction0.068119469258
2.61-2.750.409293.70.322748neutron diffraction0.076118177765.8
2.75-2.920.34343.90.32830neutron diffraction0.058118386473
2.92-3.150.378505.10.311933neutron diffraction0.053121198381.2
3.15-3.470.3484240.3191009neutron diffraction0.0541185105188.7
3.47-3.970.3475650.2841068neutron diffraction0.0461218112492.3
3.97-50.239514.40.3011097neutron diffraction0.0331208114895
5-31.790.5076150.4631159neutron diffraction0.0651284122095
1.82-1.910.326614.90.3261179x-ray diffraction0.0423040124040.8
1.91-2.010.3321105.10.3282066x-ray diffraction0.0323032217671.8
2.01-2.130.2921224.80.3142411x-ray diffraction0.0263041253383.3
2.13-2.30.29415960.3022509x-ray diffraction0.0233047266887.6
2.3-2.530.321124.10.2972652x-ray diffraction0.033066276490.2
2.53-2.890.2714250.2762720x-ray diffraction0.0233063286293.4
2.89-3.640.2831404.80.2452804x-ray diffraction0.0243089294495.3
3.64-31.790.1851514.90.192915x-ray diffraction0.0153205306695.6

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