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- PDB-1zos: Structure of 5'-methylthionadenosine/S-Adenosylhomocysteine nucle... -

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Basic information

Entry
Database: PDB / ID: 1zos
TitleStructure of 5'-methylthionadenosine/S-Adenosylhomocysteine nucleosidase from S. pneumoniae with a transition-state inhibitor MT-ImmA
Components5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / nucleosidase / pneumoniae / transition state / inhibitor
Function / homology
Function and homology information


adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / 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-MTM / adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShi, W. / Singh, V. / Zhen, R. / Tyler, P.C. / Furneaux, R.H. / Almo, S.C. / Schramm, V.L.
CitationJournal: Biochemistry / Year: 2006
Title: Structure and inhibition of a quorum sensing target from Streptococcus pneumoniae.
Authors: Singh, V. / Shi, W. / Almo, S.C. / Evans, G.B. / Furneaux, R.H. / Tyler, P.C. / Painter, G.F. / Lenz, D.H. / Mee, S. / Zheng, R. / Schramm, V.L.
History
DepositionMay 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 23, 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: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
C: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
D: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
E: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
F: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,98412
Polymers148,2006
Non-polymers1,7846
Water10,665592
1
A: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9954
Polymers49,4002
Non-polymers5952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-35 kcal/mol
Surface area16660 Å2
MethodPISA
2
C: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
D: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9954
Polymers49,4002
Non-polymers5952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-37 kcal/mol
Surface area16790 Å2
MethodPISA
3
E: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
F: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9954
Polymers49,4002
Non-polymers5952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-36 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.571, 138.958, 84.755
Angle α, β, γ (deg.)90, 117.921, 90
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is dimer (A/B, C/D, E/F)

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Components

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


Mass: 24699.943 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Species: Streptococcus pneumoniae / Strain: ATCC BAA-255 / R6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8DQ16, methylthioadenosine nucleosidase
#2: Chemical
ChemComp-MTM / (3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL / (1S)-1-(9-DEAZAADENIN-9-YL)-1,4,5-TRIDEOXY-1,4-IMINO-5-METHYLTHIO-D-RIBITOL


Mass: 297.377 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H19N5O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.83 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: MPD, CaCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 193063 / Num. obs: 193063 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.048 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 3 / Num. unique all: 16927 / Rsym value: 0.253 / % possible all: 78.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JYS

1jys


Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 13699 -random
Rwork0.193 ---
obs-184285 85.2 %-
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å2-1.28 Å2
2--3.43 Å20 Å2
3----2.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10410 0 120 592 11122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.65
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.251 1839 -
Rwork0.226 --
obs-23234 69.8 %

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