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- PDB-5kb3: 1.4 A resolution structure of Helicobacter Pylori MTAN in complex... -

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Basic information

Entry
Database: PDB / ID: 5kb3
Title1.4 A resolution structure of Helicobacter Pylori MTAN in complexed with p-ClPh-DADMe-ImmA
ComponentsAminodeoxyfutalosine nucleosidase
KeywordsHYDROLASE / nucleosidase / helicobacter pylori / neutron crystallography
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 / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsBanco, M.T. / Ronning, D.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Aeronautic Space Administration (NASA, United States)N-123528-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105084 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
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Dec 11, 2019Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3903
Polymers24,9761
Non-polymers4142
Water4,360242
1
A: Aminodeoxyfutalosine nucleosidase
hetero molecules

A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7806
Polymers49,9522
Non-polymers8284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area3680 Å2
ΔGint-40 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.207, 81.207, 67.254
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-453-

HOH

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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: 24975.754 Da / Num. of mol.: 1
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-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES pH 7.5, 18 % w/v polyethylene glycol 550 monomethyl ether, and 95 mM magnesium chloride hexahydrate.

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.399→34.76 Å / Num. obs: 50579 / % possible obs: 99.3 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.445 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NM5

3nm5


Resolution: 1.399→34.76 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1701 2007 3.97 %
Rwork0.139 --
obs0.1402 50546 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 27 242 2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051824
X-RAY DIFFRACTIONf_angle_d0.8212461
X-RAY DIFFRACTIONf_dihedral_angle_d18.017676
X-RAY DIFFRACTIONf_chiral_restr0.078282
X-RAY DIFFRACTIONf_plane_restr0.004311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3986-1.43360.20561420.15273396X-RAY DIFFRACTION98
1.4336-1.47230.17961420.13323411X-RAY DIFFRACTION99
1.4723-1.51570.13921390.11063417X-RAY DIFFRACTION99
1.5157-1.56460.15741420.10593443X-RAY DIFFRACTION99
1.5646-1.62050.12421400.10833426X-RAY DIFFRACTION99
1.6205-1.68540.15611430.11023421X-RAY DIFFRACTION99
1.6854-1.76210.16561440.12053465X-RAY DIFFRACTION100
1.7621-1.8550.16311430.12723466X-RAY DIFFRACTION100
1.855-1.97120.16121420.12733466X-RAY DIFFRACTION100
1.9712-2.12340.15031420.12693486X-RAY DIFFRACTION100
2.1234-2.3370.15561400.13523512X-RAY DIFFRACTION100
2.337-2.67510.17011460.15093497X-RAY DIFFRACTION100
2.6751-3.36990.18871480.16043561X-RAY DIFFRACTION100
3.3699-34.77060.18251540.14783572X-RAY DIFFRACTION98

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