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- PDB-2dds: Crystal structure of sphingomyelinase from Bacillus cereus with c... -

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Basic information

Entry
Database: PDB / ID: 2dds
TitleCrystal structure of sphingomyelinase from Bacillus cereus with cobalt ion
ComponentsSphingomyelin phosphodiesterase
KeywordsHYDROLASE / DNase I like folding / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / killing of cells of another organism / extracellular region
Similarity search - Function
Sphingomyelin phosphodiesterase 2-like / Sphingomyelinase C/phospholipase C / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Sphingomyelinase C
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAgo, H. / Oda, M. / Takahashi, M. / Tsuge, H. / Ochi, S. / Katunuma, N. / Miyano, M. / Sakurai, J. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus.
Authors: Ago, H. / Oda, M. / Takahashi, M. / Tsuge, H. / Ochi, S. / Katunuma, N. / Miyano, M. / Sakurai, J.
History
DepositionFeb 2, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingomyelin phosphodiesterase
B: Sphingomyelin phosphodiesterase
C: Sphingomyelin phosphodiesterase
D: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,07916
Polymers137,3724
Non-polymers70712
Water20,1051116
1
A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5204
Polymers34,3431
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5204
Polymers34,3431
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5204
Polymers34,3431
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5204
Polymers34,3431
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.090, 72.670, 78.060
Angle α, β, γ (deg.)112.00, 90.05, 116.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Sphingomyelin phosphodiesterase / / sphingomyelinase


Mass: 34343.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: IAM 1029 / Plasmid: pHY300PLK / Production host: Bacillus subtilis (bacteria) / Strain (production host): ISW1214
References: UniProt: P11889, sphingomyelin phosphodiesterase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1116 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 6.5
Details: 18% (w/v) PEG 8000, 0.2M cobalt chloride, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→35.8 Å / Num. all: 103230 / Num. obs: 103230 / % possible obs: 91.1 % / Biso Wilson estimate: 15.8 Å2
Reflection shellResolution: 1.77→1.83 Å / % possible all: 83.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.67 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1415548.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 9874 10 %RANDOM
Rwork0.202 ---
obs0.202 98540 91.6 %-
all-98540 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.0242 Å2 / ksol: 0.324019 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å2-0.3 Å20.15 Å2
2---2.09 Å21.07 Å2
3---3.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9320 0 12 1116 10448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 1549 10.3 %
Rwork0.268 13461 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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