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- PDB-5jpc: Joint X-ray/neutron structure of MTAN complex with Formycin A -

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Basic information

Entry
Database: PDB / ID: 5jpc
TitleJoint X-ray/neutron structure of MTAN complex with Formycin A
ComponentsAminodeoxyfutalosine nucleosidase
KeywordsHYDROLASE / Neutron / Nucleosidase / Joint Neutron and X-ray / Helicobacter pylori
Function / homology
Function and homology information


aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / nucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / 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
DEUTERATED WATER / Chem-FMC / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.5 Å
AuthorsBanco, M.T. / Kovalevsky, A.Y. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Space - X 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
DepositionMay 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site

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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)25,1862
Polymers24,9191
Non-polymers2671
Water95553
1
A: Aminodeoxyfutalosine nucleosidase
hetero molecules

A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3724
Polymers49,8372
Non-polymers5342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_467y-1,x+1,-z+21
Buried area17690 Å2
ΔGint-13 kcal/mol
Surface area16090 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-631-

DOD

21A-652-

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: 24918.703 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: Chemical ChemComp-FMC / (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 53 / 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
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 276.15 K / Method: evaporation / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 15-20% w/v PEG550, 95 mM magnesium chloride hexahydrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12951
22961
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D12.8-4.5
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
BIODIFF1IMAGE PLATEMay 16, 2015
RIGAKU RAXIS IV++2IMAGE PLATEJul 27, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.81
24.51
31.541
ReflectionResolution: 2.5→49.45 Å / Num. obs: 7143 / % possible obs: 74.5 % / Redundancy: 3.5 % / Net I/σ(I): 2.6
Reflection shellHighest resolution: 2.2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
nCNS1.0.0refinement
HKL-3000data reduction
SCALEPACKdata scaling
REFMACphasing
Refinement

Biso max: 80.16 Å2 / Biso mean: 33.61 Å2 / Biso min: 5.24 Å2 / Cross valid method: FREE R-VALUE / Bsol: 10 Å2 / ksol: 0.338401 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
2.5-36.02NEUTRON DIFFRACTION0.2660.0170.282245965752604.754.51
2.1-35.43X-RAY DIFFRACTION0.2350.010.20860016126124714.877.32
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.440.42
Luzzati d res low-5
Luzzati sigma a0.610.6
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.30.26
Luzzati d res low-5
Luzzati sigma a0.270.23
Refine funct minimized
Refine-IDType
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
X-RAY DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2.5→36.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 19 53 1823
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.008
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg19.1
NEUTRON DIFFRACTIONx_torsion_impr_deg0.79
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg19.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.79
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 (%)
2.5-2.610.317133.40.37366NEUTRON DIFFRACTION0.088119037931.8
2.61-2.750.48204.60.351411NEUTRON DIFFRACTION0.107118143136.5
2.75-2.920.312275.90.346433NEUTRON DIFFRACTION0.06118346038.9
2.92-3.150.288274.80.34530NEUTRON DIFFRACTION0.055121155746
3.15-3.470.295243.80.378610NEUTRON DIFFRACTION0.06118463453.5
3.47-3.970.272486.10.283743NEUTRON DIFFRACTION0.039121779164.9
3.97-50.171434.60.207902NEUTRON DIFFRACTION0.026120994578.2
5-36.020.2634340.2511020NEUTRON DIFFRACTION0.041285106382.7
2.1-2.20.331275.20.252496X-RAY DIFFRACTION0.064199152326.3
2.2-2.310.296554.80.2561099X-RAY DIFFRACTION0.041983115458.2
2.31-2.460.256805.40.2361408X-RAY DIFFRACTION0.0291978148875.2
2.46-2.650.264694.20.2391568X-RAY DIFFRACTION0.0322011163781.4
2.65-2.910.243925.20.2451683X-RAY DIFFRACTION0.0252002177588.7
2.91-3.330.305884.70.2241781X-RAY DIFFRACTION0.0332028186992.2
3.33-4.20.224924.70.1861860X-RAY DIFFRACTION0.0232028195296.3
4.2-35.430.178974.70.1761976X-RAY DIFFRACTION0.0182123207397.6

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