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- PDB-4yo8: Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S... -

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Basic information

Entry
Database: PDB / ID: 4yo8
TitleCrystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)(hexyl)amino)methanol
ComponentsAminodeoxyfutalosine nucleosidase
KeywordsHydrolase/Hydrolase Inhibitor / hydrolase / Hydrolase-Hydrolase Inhibitor complex
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
Chem-4EZ / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCameron, S.A. / Wang, S. / Almo, S.C. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM041916 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2015
Title: New Antibiotic Candidates against Helicobacter pylori.
Authors: Wang, S. / Cameron, S.A. / Clinch, K. / Evans, G.B. / Wu, Z. / Schramm, V.L. / Tyler, P.C.
#1: Journal: Biochemistry / Year: 2012
Title: A picomolar transition state analogue inhibitor of MTAN as a specific antibiotic for Helicobacter pylori.
Authors: Wang, S. / Haapalainen, A.M. / Yan, F. / Du, Q. / Tyler, P.C. / Evans, G.B. / Rinaldo-Matthis, A. / Brown, R.L. / Norris, G.E. / Almo, S.C. / Schramm, V.L.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminodeoxyfutalosine nucleosidase
B: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3945
Polymers53,7742
Non-polymers6203
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-46 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.091, 69.446, 65.566
Angle α, β, γ (deg.)90.000, 113.080, 90.000
Int Tables number4
Space group name H-MP1211

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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: 26886.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: mtnN, mtn, jhp_0082 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9ZMY2, aminodeoxyfutalosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-4EZ / {[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl](hexyl)amino}methanol


Mass: 277.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H23N5O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.54 Å3/Da / Density % sol: 51.48 % / Description: Needles
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Protein (10 mg/mL); Reservoir (0.2 M sodium malonate pH 7.0 and 20 % (w/v) PEG 3350); Cryoprotection (20% (v/v) glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2014
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 31369 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.181 / Net I/av σ(I): 23.743 / Net I/σ(I): 10.9 / Num. measured all: 115268
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.1-2.143.30.5882.3215361.00599.3
2.14-2.183.40.58615871.04999.6
2.18-2.223.50.65815311.01699.9
2.22-2.263.60.5715871.233100
2.26-2.313.70.48915481.053100
2.31-2.373.70.47415481.066100
2.37-2.423.80.44815741.066100
2.42-2.493.80.36515621.066100
2.49-2.563.80.28715681.04499.9
2.56-2.653.80.23115611.05599.9
2.65-2.743.80.1915671.042100
2.74-2.853.80.1415641.034100
2.85-2.983.80.11715651.088100
2.98-3.143.80.08815701.081100
3.14-3.333.80.06815671.223100
3.33-3.593.80.0615711.6100
3.59-3.953.70.05315752.053100
3.95-4.523.70.03916021.678100
4.52-5.73.60.02715841.059100
5.7-503.70.02316021.03598.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FFS

4ffs


Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.102 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.171 / SU Rfree Cruickshank DPI: 0.1709 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 1578 5 %RANDOM
Rwork0.1873 ---
obs0.1891 29762 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.91 Å2 / Biso mean: 37.684 Å2 / Biso min: 20.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å2-3.27 Å2
2--4.75 Å20 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 41 100 3777
Biso mean--34.46 34.36 -
Num. residues----480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193747
X-RAY DIFFRACTIONr_bond_other_d0.0010.023596
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9635059
X-RAY DIFFRACTIONr_angle_other_deg0.76838282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58525.26154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0715632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.369156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
X-RAY DIFFRACTIONr_mcbond_it1.9583.6541918
X-RAY DIFFRACTIONr_mcbond_other1.9593.6531917
X-RAY DIFFRACTIONr_mcangle_it2.8935.4722394
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 143 -
Rwork0.311 2090 -
all-2233 -
obs--97.68 %

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