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- PDB-3nm4: Helicobacter pylori MTAN -

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Basic information

Entry
Database: PDB / ID: 3nm4
TitleHelicobacter pylori MTAN
ComponentsMTA/SAH nucleosidase
KeywordsHYDROLASE / nucleosidase
Function / homology
Function and homology information


aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / methylthioadenosine nucleosidase activity / 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
Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Sep 6, 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 / 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
A: MTA/SAH nucleosidase
B: MTA/SAH nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5949
Polymers50,1002
Non-polymers4957
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-4 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.310, 81.310, 135.485
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 25049.900 Da / Num. of mol.: 2
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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 52.34 %
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: 1.7→50 Å / Num. obs: 57817 / % possible obs: 100 % / Observed criterion σ(F): 1 / Redundancy: 14.1 % / Biso Wilson estimate: 16.28 Å2 / Rsym value: 0.071 / Net I/σ(I): 9.3

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Processing

Software
NameVersionClassification
EPMRphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BL6

3bl6


Resolution: 1.7→38.94 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 2881 5.08 %random
Rwork0.17 ---
obs0.1713 56757 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.646 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2713 Å2-0 Å2-0 Å2
2--1.2713 Å20 Å2
3----2.5426 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 32 328 3814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063607
X-RAY DIFFRACTIONf_angle_d1.0054862
X-RAY DIFFRACTIONf_dihedral_angle_d13.6771331
X-RAY DIFFRACTIONf_chiral_restr0.073567
X-RAY DIFFRACTIONf_plane_restr0.004618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6986-1.75930.19522720.16445095X-RAY DIFFRACTION94
1.7593-1.82970.18632680.16225218X-RAY DIFFRACTION96
1.8297-1.9130.20852970.16835233X-RAY DIFFRACTION97
1.913-2.01390.21012940.1635345X-RAY DIFFRACTION98
2.0139-2.140.19862870.15745383X-RAY DIFFRACTION99
2.14-2.30530.18692790.15675398X-RAY DIFFRACTION99
2.3053-2.53720.18683030.16465423X-RAY DIFFRACTION99
2.5372-2.90420.17852770.16495500X-RAY DIFFRACTION99
2.9042-3.65860.20642820.17635545X-RAY DIFFRACTION100
3.6586-38.94990.19173220.17735736X-RAY DIFFRACTION100

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