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- PDB-5ccd: Joint X-ray/neutron structure of MTAN D198N complex with SAH -

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Basic information

Entry
Database: PDB / ID: 5ccd
TitleJoint X-ray/neutron structure of MTAN D198N complex with SAH
ComponentsAminodeoxyfutalosine nucleosidase
KeywordsHYDROLASE / Helicobacter pylori / Neutron / S-Adenosylhomocysteine / N-Glycosyl Hydrolases
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 methylthioadenosine / menaquinone biosynthetic process
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
DEUTERATED WATER / S-ADENOSYL-L-HOMOCYSTEINE / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Derived calculations / Structure summary
Category: pdbx_audit_support / pdbx_struct_special_symmetry / struct_keywords
Item: _pdbx_audit_support.funding_organization / _struct_keywords.pdbx_keywords
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5132
Polymers25,1291
Non-polymers3841
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aminodeoxyfutalosine nucleosidase
hetero molecules

A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0274
Polymers50,2582
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area21890 Å2
ΔGint-6 kcal/mol
Surface area16170 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-449-

DOD

21A-468-

DOD

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Components

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


Mass: 25128.936 Da / Num. of mol.: 1 / Mutation: D198N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain J99 / ATCC 700824) (bacteria)
Strain: J99 / ATCC 700824 / Gene: mtnN, mtn, jhp_0082 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ZMY2, aminodeoxyfutalosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 550 MME, Magnesium Chloride Hexahydrate and HEPES pH 7

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceBeamlineTypeIDWavelength
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORIMAGINE22.8 - 4.5
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 7, 2014 / Details: OSMIC VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
34.51
Reflection

Entry-ID: 5CCD

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.2-401369697.14.30.076119.5
2.6-40717574.73.50.19623.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.89-2.284.40.6272.3195.2
2.49-2.632.60.3371.7258.5

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Processing

Software
NameVersionClassification
CNSnCNS 1.0.0refinement
DENZOdata processing
SCALEPACKdata scaling
HKL-3000data processing
Cootmodel building
CNS1.0.0refinement
Omodel building
PHENIXphasing
nCNS1.0.0refinement
Refinement

R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / σ(F): 3 / Method to determine structure: MOLECULAR REPLACEMENT

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
2.2-40X-RAY DIFFRACTION0.2390.0070.2031035106161074.71
2.6-30.02NEUTRON DIFFRACTION0.2140.0210.20148273149.7762
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.30.26
Luzzati d res low-5
Luzzati sigma a0.30.26
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.690.51
Luzzati d res low-5
Luzzati sigma a1.481.04
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 26 77 1858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg16.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.77
NEUTRON DIFFRACTIONx_bond_d0.008
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg16.7
NEUTRON DIFFRACTIONx_torsion_impr_deg0.77
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
2.2-2.30.2634211.10.248380X-RAY DIFFRACTION0.04121.9
2.6-2.720.51638110.439344NEUTRON DIFFRACTION0.08433

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