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- PDB-4g41: Crystal structure of s-adenosylhomocysteine nucleosidase from str... -

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Basic information

Entry
Database: PDB / ID: 4g41
TitleCrystal structure of s-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with 5-methylthiotubericidin
ComponentsMTA/SAH nucleosidase
KeywordsHYDROLASE / MIXED ALPHA/BETA / S-ADENOSYLHOMOCYSTEINE / CLEAVAGE
Function / homologyNucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 5'-DEOXY-5'-METHYLTHIOADENOSINE / :
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPonniah, K. / Norris, G.E. / Anderson, B.F. / Brown, R.L. / Tyler, P.C. / Evans, G.B. / Frohlich, R.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of s-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with 5-methylthiotubericidin;
Authors: Ponniah, K. / Norris, G.E. / Anderson, B.F. / Brown, R.L. / Tyler, P.C. / Evans, G.B. / Frohlich, R.
History
DepositionJul 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MTA/SAH nucleosidase
B: MTA/SAH nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6953
Polymers50,3982
Non-polymers2971
Water14,142785
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-31 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.735, 72.345, 116.246
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


Mass: 25198.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: ATCC 10782 / Gene: HMPREF0841_1463, mtn N, mtnN / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E0PXI9, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG MME 5000, 0.1M MES, 0.2M AMMONIUM SULPHATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 20, 2008 / Details: MIRRORS
RadiationMonochromator: OPTICS CAPILLIARY / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→20.62 Å / Num. all: 66215 / Num. obs: 66215 / % possible obs: 87.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.91 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 27.3
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.4 / % possible all: 21.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: S.AUREUS MTAN

Resolution: 1.45→20.47 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.998 / SU ML: 0.039 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.078 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE ADDED IN THIER RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19744 3357 5.1 %RANDOM
Rwork0.16181 ---
all0.1636 66215 --
obs0.1636 62797 87.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.251 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 20 785 4343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.023695
X-RAY DIFFRACTIONr_angle_refined_deg2.3141.9555023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83425.43151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9915622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.138159
X-RAY DIFFRACTIONr_chiral_restr0.1570.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022763
LS refinement shellResolution: 1.448→1.485 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.774 54 -
Rwork0.658 1062 -
obs-1062 20.45 %

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