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- PDB-5a3c: Crystal structure of the ADP-ribosylating sirtuin (SirTM) from St... -

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Basic information

Entry
Database: PDB / ID: 5a3c
TitleCrystal structure of the ADP-ribosylating sirtuin (SirTM) from Streptococcus pyogenes in complex with NAD
ComponentsSIR2 FAMILY PROTEIN
KeywordsTRANSFERASE / ADP-RIBOSYLTRANSFERASE / METALLOPROTEIN / NAD-DEPENDENT / LIPOYLATION / REGULATORY ENZYME / ROSSMANN FOLD / ZINC BINDING / ROS DEFENSE
Function / homologySirtuin, catalytic core small domain superfamily / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / nucleotide binding / metal ion binding / GLYCINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SIR2 family protein
Function and homology information
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsRack, J.G.M. / Morra, R. / Barkauskaite, E. / Kraehenbuehl, R. / Ariza, A. / Qu, Y. / Ortmayer, M. / Leidecker, O. / Cameron, D.R. / Matic, I. ...Rack, J.G.M. / Morra, R. / Barkauskaite, E. / Kraehenbuehl, R. / Ariza, A. / Qu, Y. / Ortmayer, M. / Leidecker, O. / Cameron, D.R. / Matic, I. / Peleg, A.Y. / Leys, D. / Traven, A. / Ahel, I.
CitationJournal: Mol.Cell / Year: 2015
Title: Identification of a Class of Protein Adp-Ribosylating Sirtuins in Microbial Pathogens.
Authors: Rack, J.G. / Morra, R. / Barkauskaite, E. / Kraehenbuehl, R. / Ariza, A. / Qu, Y. / Ortmayer, M. / Leidecker, O. / Cameron, D.R. / Matic, I. / Peleg, A.Y. / Leys, D. / Traven, A. / Ahel, I.
History
DepositionMay 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Atomic model / Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIR2 FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2358
Polymers35,1571
Non-polymers1,0787
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.880, 41.480, 51.260
Angle α, β, γ (deg.)99.55, 93.61, 92.98
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SIR2 FAMILY PROTEIN / ADP-RIBOSYLATING SIRTUIN / SIRTM


Mass: 35156.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: MANFREDO / Variant: SEROTYPE M5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q1JGN6, NAD+ ADP-ribosyltransferase

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Non-polymers , 5 types, 164 molecules

#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.14 Å3/Da / Density % sol: 43.44 %
Description: SAD DATA NOT DEPOSITED. SAD STRUCTURE WAS USED TO SUBSEQUENTLY SOLVE NATIVE STRUCTURES VIA MOLECULAR REPLACEMENT.
Crystal growpH: 8
Details: CRYSTALLIZATION CONDITIONS: 0.1 M AMINO ACIDS, 0.1 M BUFFER SYSTEM 1 (PH 6.5), 30.00% (V/V) EDO_P8K (THESE ARE COMPONENTS OF THE MORPHEUS SCREEN FROM MOLECULAR DIMENSIONS)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.03→40.82 Å / Num. obs: 17229 / % possible obs: 97.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.8
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.9 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.03→40.82 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.456 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS AND U VALUES WERE REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 856 5 %RANDOM
Rwork0.17559 ---
obs0.17843 16372 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.811 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0.44 Å2-0.42 Å2
2--1.2 Å2-0.02 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.03→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 68 157 2570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192534
X-RAY DIFFRACTIONr_bond_other_d0.0010.022336
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9513448
X-RAY DIFFRACTIONr_angle_other_deg0.73435385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1715302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59424.733131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68115419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.283159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_it1.232.311172
X-RAY DIFFRACTIONr_mcbond_other1.2152.2861162
X-RAY DIFFRACTIONr_mcangle_it1.9763.4341462
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6412.5691362
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7893.7681978
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: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 61 -
Rwork0.237 1199 -
obs--95.31 %

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