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- PDB-5k1z: Joint X-ray/neutron structure of MTAN complex with p-ClPh-Thio-DA... -

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Basic information

Entry
Database: PDB / ID: 5k1z
TitleJoint X-ray/neutron structure of MTAN complex with p-ClPh-Thio-DADMe-ImmA
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 / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / 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
Chem-4CT / DEUTERATED WATER / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.6 Å
AuthorsBanco, M.T. / Kovalevsky, A.Y. / Ronning, D.R.
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 18, 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)25,3092
Polymers24,9191
Non-polymers3901
Water1,04558
1
A: Aminodeoxyfutalosine nucleosidase
hetero molecules

A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6174
Polymers49,8372
Non-polymers7802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area17700 Å2
ΔGint-11 kcal/mol
Surface area16480 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-426-

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-4CT / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol


Mass: 389.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20ClN5OS
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 277.15 K / Method: evaporation / pH: 7
Details: 100 mM HEPES, pH 7.0, 28-30% w/v PEG550 MME, 50 mM magnesium chloride hexahydrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D12.8-4.5
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
MAATEL IMAGINE1IMAGE PLATEJul 24, 2015
RIGAKU RAXIS IV++2IMAGE PLATEAug 4, 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: 2.6→31.88 Å / Num. obs: 6426 / % possible obs: 75.1 % / Redundancy: 3.1 % / Net I/σ(I): 3.3
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

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

Biso max: 94.37 Å2 / Biso mean: 41.83 Å2 / Biso min: 9.71 Å2 / Cross valid method: FREE R-VALUE / Bsol: 31.7033 Å2 / ksol: 0.43874 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
2.6-31.79NEUTRON DIFFRACTION0.2870.0190.253219859748374.556.31
2.25-35.43X-RAY DIFFRACTION0.2580.0120.20548313161101964.777.52
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.50.43
Luzzati d res low-5
Luzzati sigma a0.951.01
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.330.28
Luzzati d res low-5
Luzzati sigma a0.340.29
Refine funct minimized
Refine-IDType
NEUTRON DIFFRACTIONJoint X-ray/neutron MTAN_DADMe-ImmA
X-RAY DIFFRACTIONJoint X-ray/neutron MTAN_DADMe-ImmA
Refinement stepCycle: LAST / Resolution: 2.6→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 26 58 1835
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.009
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg15.9
NEUTRON DIFFRACTIONx_torsion_impr_deg0.8
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg15.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.8
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 (%)
2.6-2.720.566113.40.384315NEUTRON DIFFRACTION0.171104432631.2
2.72-2.860.43174.60.404352NEUTRON DIFFRACTION0.104105536935
2.86-3.040.39245.80.376391NEUTRON DIFFRACTION0.08106641538.9
3.04-3.280.336356.80.36478NEUTRON DIFFRACTION0.057106351348.3
3.28-3.60.396264.30.334582NEUTRON DIFFRACTION0.078107660856.5
3.6-4.120.273212.80.239737NEUTRON DIFFRACTION0.059107275870.7
4.12-5.190.225384.30.166851NEUTRON DIFFRACTION0.036109088981.6
5.19-31.790.217474.90.21912NEUTRON DIFFRACTION0.032114195984
2.25-2.350.339284.40.262602X-RAY DIFFRACTION0.064160763039.2
2.35-2.480.312495.30.257875X-RAY DIFFRACTION0.045162792456.8
2.48-2.630.277595.10.2571087X-RAY DIFFRACTION0.0361620114670.7
2.63-2.830.272584.50.2441223X-RAY DIFFRACTION0.0361638128178.2
2.83-3.120.327654.60.2431333X-RAY DIFFRACTION0.0411633139885.6
3.12-3.570.276795.20.2211441X-RAY DIFFRACTION0.0311646152092.3
3.57-4.50.225674.20.1761534X-RAY DIFFRACTION0.0271662160196.3
4.5-35.430.226784.60.1741618X-RAY DIFFRACTION0.0261739169697.5

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