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- PDB-1s5p: Structure and substrate binding properties of cobB, a Sir2 homolo... -

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Basic information

Entry
Database: PDB / ID: 1s5p
TitleStructure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.
Components
  • HISTONE H4 (RESIDUES 12-19)
  • NAD-dependent deacetylase
KeywordsHYDROLASE / protein deacetylase / Sir2 homologue
Function / homology
Function and homology information


lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / cyclic-di-GMP binding / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / NAD+ ADP-ribosyltransferase activity / NAD+ binding ...lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / cyclic-di-GMP binding / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / NAD+ ADP-ribosyltransferase activity / NAD+ binding / chemotaxis / defense response to virus / protein homodimerization activity / zinc ion binding / cytoplasm
Similarity search - Function
Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD-dependent protein deacylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 Å
AuthorsZhao, K. / Chai, X. / Marmorstein, R.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure and Substrate Binding Properties of cobB, a Sir2 Homolog Protein Deacetylase from Eschericia coli.
Authors: Zhao, K. / Chai, X. / Marmorstein, R.
History
DepositionJan 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent deacetylase
B: HISTONE H4 (RESIDUES 12-19)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1093
Polymers27,0442
Non-polymers651
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-43 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.911, 93.911, 61.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NAD-dependent deacetylase / Regulatory protein SIR2 homolog


Mass: 26088.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NPDA, COBB, B1120 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(de3)
References: UniProt: P75960, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide HISTONE H4 (RESIDUES 12-19)


Mass: 955.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic
#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 / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.67 Å3/Da / Density % sol: 53.56 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlcobB1drop
21.0 mMpeptide1drop
325 %PEG33501reservoir
4100 mMBis-Tris1reservoirpH6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9
SYNCHROTRONAPS 19-ID21.28
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.281
ReflectionResolution: 1.96→50 Å / Num. obs: 20061 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.034 / Net I/σ(I): 55.5
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1950 / Rsym value: 0.244 / % possible all: 98.6
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.96→29.7 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 928333.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1359 6.9 %RANDOM
Rwork0.234 ---
obs0.234 19826 97.6 %-
all-19826 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.6041 Å2 / ksol: 0.375912 e/Å3
Displacement parametersBiso mean: 49.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.96→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 1 229 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.38
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.831.5
X-RAY DIFFRACTIONc_mcangle_it5.42
X-RAY DIFFRACTIONc_scbond_it5.282
X-RAY DIFFRACTIONc_scangle_it7.222.5
LS refinement shellResolution: 1.96→2.08 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 208 6.7 %
Rwork0.308 2895 -
obs-3103 93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REPPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.38

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