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- PDB-3nm6: Helicobacter pylori MTAN complexed with adenine and tris -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3nm6
TitleHelicobacter pylori MTAN complexed with adenine and tris
ComponentsMTA/SAH nucleosidase
KeywordsHYDROLASE / nucleosidase
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
ADENINE / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.602 Å
AuthorsRonning, D.R. / Iacopelli, N.M.
CitationJournal: Protein Sci. / Year: 2010
Title: Enzyme-ligand interactions that drive active site rearrangements in the Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.
Authors: Ronning, D.R. / Iacopelli, N.M. / Mishra, V.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: MTA/SAH nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5557
Polymers25,0501
Non-polymers5066
Water2,846158
1
B: MTA/SAH nucleosidase
hetero molecules

B: MTA/SAH nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,11114
Polymers50,1002
Non-polymers1,01112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557x-y,-y,-z+7/31
Buried area5720 Å2
ΔGint5 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.350, 81.350, 67.595
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
11B-322-

HOH

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Components

#1: Protein MTA/SAH nucleosidase / 5'-methylthioadenosine nucleosidase / S-adenosylhomocysteine nucleosidase


Mass: 25049.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: jhp_0082, mtn, mtnN, Pfs / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9ZMY2, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16 % w/v PEG 8000, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 33924 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 17.51 Å2 / Rsym value: 0.05 / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.602→34.852 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1707 1650 4.95 %random
Rwork0.1414 ---
obs0.1429 33313 96.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.111 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7712 Å20 Å2-0 Å2
2--3.7712 Å20 Å2
3----7.5423 Å2
Refinement stepCycle: LAST / Resolution: 1.602→34.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 34 158 1943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051858
X-RAY DIFFRACTIONf_angle_d0.9452496
X-RAY DIFFRACTIONf_dihedral_angle_d13.3678
X-RAY DIFFRACTIONf_chiral_restr0.066290
X-RAY DIFFRACTIONf_plane_restr0.004317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6016-1.65880.16441480.09372959X-RAY DIFFRACTION92
1.6588-1.72520.13441640.08552970X-RAY DIFFRACTION93
1.7252-1.80370.14171370.08413127X-RAY DIFFRACTION96
1.8037-1.89880.15181720.08913125X-RAY DIFFRACTION97
1.8988-2.01780.15211850.09593104X-RAY DIFFRACTION97
2.0178-2.17350.1491550.10923220X-RAY DIFFRACTION98
2.1735-2.39220.15561640.12363228X-RAY DIFFRACTION99
2.3922-2.73830.17021900.14853214X-RAY DIFFRACTION99
2.7383-3.44940.18761650.16153296X-RAY DIFFRACTION100
3.4494-34.85990.17941700.16563420X-RAY DIFFRACTION99

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