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- PDB-4bn0: Structure of futalosine hydrolase mutant of Helicobacter pylori s... -

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Basic information

Entry
Database: PDB / ID: 4bn0
TitleStructure of futalosine hydrolase mutant of Helicobacter pylori strain 26695
ComponentsMTA/SAH NUCLEOSIDASE
KeywordsHYDROLASE
Function / homology
Function and homology information


aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / L-methionine salvage from S-adenosylmethionine / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / 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: 2.11 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
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
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
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
C: MTA/SAH NUCLEOSIDASE
D: MTA/SAH NUCLEOSIDASE


Theoretical massNumber of molelcules
Total (without water)109,6264
Polymers109,6264
Non-polymers00
Water2,972165
1
A: MTA/SAH NUCLEOSIDASE
B: MTA/SAH NUCLEOSIDASE


Theoretical massNumber of molelcules
Total (without water)54,8132
Polymers54,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-27.7 kcal/mol
Surface area18110 Å2
MethodPISA
2
C: MTA/SAH NUCLEOSIDASE
D: MTA/SAH NUCLEOSIDASE


Theoretical massNumber of molelcules
Total (without water)54,8132
Polymers54,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-27.5 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.230, 75.690, 97.010
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27406.428 Da / Num. of mol.: 4 / Mutation: YES
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.99 Å3/Da / Density % sol: 38.29 % / Description: A BATCH OF BAD QUALITY IMAGES WAS REMOVED
Crystal growDetails: 0.1 M HEPES PH 7.5, 25% PEG-3350, 0.2 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.11→39.64 Å / Num. obs: 48788 / % possible obs: 95.1 % / Observed criterion σ(I): 6 / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.9
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BMX

4bmx


Resolution: 2.11→39.674 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.896 / SU B: 13.433 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.275 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 2425 5.03 %RANDOM
Rwork0.2092 ---
obs0.212 48768 94.662 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.795 Å2
Baniso -1Baniso -2Baniso -3
1-0.668 Å20 Å20.162 Å2
2--0.545 Å20 Å2
3----1.075 Å2
Refinement stepCycle: LAST / Resolution: 2.11→39.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6689 0 0 165 6854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196799
X-RAY DIFFRACTIONr_bond_other_d0.0010.026636
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9599191
X-RAY DIFFRACTIONr_angle_other_deg0.901315249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61625.323263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.882151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8081512
X-RAY DIFFRACTIONr_chiral_restr0.0990.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027648
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021476
X-RAY DIFFRACTIONr_nbd_refined0.2220.21357
X-RAY DIFFRACTIONr_nbd_other0.1620.232
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23185
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2118
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_it0.7230.8893547
X-RAY DIFFRACTIONr_mcbond_other0.7230.8883546
X-RAY DIFFRACTIONr_mcangle_it1.2581.3244419
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7260.9763252
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2171.4394772
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: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 161 -
Rwork0.282 3551 -
obs--97.968 %
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)
10.26220.32350.1130.4497-0.03911.30390.0354-0.00110.00690.0299-0.00080.055-0.06170.2017-0.03460.1877-0.0117-0.00420.29070.01590.075126.50415.8166.855
21.3180.3426-0.43660.3930.51511.4634-0.10510.17760.03470.0514-0.02420.06070.1925-0.18910.12920.2167-0.04160.01060.28-0.00130.05917.811-0.473-9.077
30.55510.0995-0.19850.0544-0.06081.6917-0.120.0667-0.0308-0.01140.0539-0.06810.0595-0.63770.06610.1577-0.0723-0.00490.5021-0.07760.1093-4.37611.10735.676
40.55310.20340.05960.0932-0.14321.52770.0043-0.0630.0316-0.0019-0.03630.00810.13020.12540.0320.22590.00040.00130.3279-0.00690.007718.6616.70553.359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 231
2X-RAY DIFFRACTION2B2 - 231
3X-RAY DIFFRACTION3C-1 - 231
4X-RAY DIFFRACTION4D2 - 231

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