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- PDB-2ddt: Crystal structure of sphingomyelinase from Bacillus cereus with m... -

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Basic information

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


sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / killing of cells of another organism / extracellular region / cytoplasm
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
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAgo, H. / Oda, M. / Tsuge, H. / 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
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,36610
Polymers68,6862
Non-polymers6808
Water9,620534
1
A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6835
Polymers34,3431
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6835
Polymers34,3431
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.844, 50.893, 59.506
Angle α, β, γ (deg.)81.87, 81.84, 79.68
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.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 6.5
Details: 18% (w/v) PEG 8000, 0.2M magnesium sulfate, 0.1mM calcium chrolide, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Dec 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 48543 / Num. obs: 48543 / % possible obs: 90.8 %
Reflection shellResolution: 1.8→1.9 Å / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.971 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23024 2438 5 %RANDOM
Rwork0.19295 ---
obs0.19478 48541 90.77 %-
all-48541 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.288 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.4 Å20.76 Å2
2---0.25 Å20.66 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 38 534 5142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224722
X-RAY DIFFRACTIONr_bond_other_d00.023998
X-RAY DIFFRACTIONr_angle_refined_deg2.1611.9416411
X-RAY DIFFRACTIONr_angle_other_deg3.63739398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0145569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41825.771227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91115771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4691510
X-RAY DIFFRACTIONr_chiral_restr0.2680.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025223
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02891
X-RAY DIFFRACTIONr_nbd_refined0.2120.21000
X-RAY DIFFRACTIONr_nbd_other0.2460.24020
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22316
X-RAY DIFFRACTIONr_nbtor_other0.1120.22085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1040.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.821.53717
X-RAY DIFFRACTIONr_mcbond_other0.3921.51156
X-RAY DIFFRACTIONr_mcangle_it2.06224654
X-RAY DIFFRACTIONr_scbond_it3.22132243
X-RAY DIFFRACTIONr_scangle_it3.9984.51757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 184 -
Rwork0.238 3483 -
obs--93.17 %

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