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- PDB-4bmx: Native structure of futalosine hydrolase of Helicobacter pylori s... -

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Basic information

Entry
Database: PDB / ID: 4bmx
TitleNative structure of futalosine hydrolase of Helicobacter pylori strain 26695
ComponentsMTA/SAH NUCLEOSIDASE
KeywordsHYDROLASE
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
ADENINE / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsKim, R.Q. / Offen, W.A. / Stubbs, K.A. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural Enzymology of Helicobacter Pylori Methylthioadenosine Nucleosidase in the Futalosine Pathway
Authors: Kim, R.Q. / Offen, W.A. / Davies, G.J. / Stubbs, K.A.
History
DepositionMay 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references / Derived calculations
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)55,1945
Polymers54,8152
Non-polymers3793
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-23 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.314, 90.573, 108.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MTA/SAH NUCLEOSIDASE / 5-METHYLTHIOADENOSINE NUCLEOSIDASE / S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE / FUTALOSINE HYDROLASE


Mass: 27407.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O24915, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.67 Å3/Da / Density % sol: 53.9 % / Description: NONE
Crystal growDetails: PROTEIN WAS CRYSTALLIZED IN 4.0 M NA/K PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→54.19 Å / Num. obs: 57414 / % possible obs: 98 % / Observed criterion σ(I): 6 / Redundancy: 10.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.8
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NM4

3nm4


Resolution: 1.76→54.249 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.791 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 2855 5.08 %RANDOM
Rwork0.1687 ---
obs0.171 57357 97.752 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.842 Å2
Baniso -1Baniso -2Baniso -3
1-0.164 Å20 Å20 Å2
2---0.005 Å20 Å2
3----0.159 Å2
Refinement stepCycle: LAST / Resolution: 1.76→54.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 26 363 3860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9684883
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8625.315143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92515638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.573158
X-RAY DIFFRACTIONr_chiral_restr0.1620.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022636
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.22091
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22528
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4711.3661849
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0152.0322308
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.891.7071758
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2942.4312566
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 219 -
Rwork0.269 3955 -
obs--96.665 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2011-0.2369-0.11670.62630.06090.3786-0.0233-0.0185-0.00150.1092-0.030.0141-0.0032-0.00110.05340.06770.00970.00630.0234-0.00190.01345.7912.95927.106
20.2724-0.1376-0.03090.7693-0.18690.07740.02830.03960.0129-0.1524-0.01920.08610.0493-0.0028-0.00910.08090.0159-0.02160.0177-0.00240.03482.05611.898-1.611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 231
2X-RAY DIFFRACTION2B-1 - 231

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