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- PDB-2uyr: Crystal structure of Bacillus cereus sphingomyelinase mutant :N57A -

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Basic information

Entry
Database: PDB / ID: 2uyr
TitleCrystal structure of Bacillus cereus sphingomyelinase mutant :N57A
ComponentsSPHINGOMYELINASE C
KeywordsHYDROLASE / N57A METAL ION OF SIDE-EDGE / BACILLUS CEREUS SPHINGOMYELINASE / HEMOLYSIS / CYTOLYSIS
Function / homology
Function and homology information


sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / killing of cells of another organism / extracellular region
Similarity search - Function
Sphingomyelinase C/phospholipase C / Sphingomyelin phosphodiesterase 2-like / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOda, M. / Tsuge, H. / Sakurai, J.
CitationJournal: To be Published
Title: Crystal Structure of Bacillus Cereus Sphingomyelinase Mutant : N57A
Authors: Oda, M. / Tsuge, H. / Sakurai, J.
History
DepositionApr 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: SPHINGOMYELINASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2962
Polymers34,2721
Non-polymers241
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.090, 63.927, 101.690
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 SPHINGOMYELINASE C / SPHINGOMYELINASE / SPHINGOMYELIN PHOSPHODIESTERASE / SMASE / SMPLC / CEREOLYSIN B


Mass: 34271.926 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: IAM 1029 / Variant: N57A / Production host: BACILLUS SUBTILIS (bacteria)
References: UniProt: P11889, sphingomyelin phosphodiesterase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN X, ASN 84 TO ALA
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.3 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M CALCIUM ACETATE 0.2 M SODIUM CACODYLATE (PH7.5) 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGING PLATE / Date: Jun 7, 2006 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→48.44 Å / Num. obs: 14493 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.33 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DDT

2ddt


Resolution: 2.4→54.15 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.142 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 724 5 %RANDOM
Rwork0.182 ---
obs0.184 13721 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→54.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 1 89 2451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222419
X-RAY DIFFRACTIONr_bond_other_d0.0590.027
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9353293
X-RAY DIFFRACTIONr_angle_other_deg0.761313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.53925.862116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71815398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.305155
X-RAY DIFFRACTIONr_chiral_restr0.1210.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021878
X-RAY DIFFRACTIONr_gen_planes_other0.0060.027
X-RAY DIFFRACTIONr_nbd_refined0.2070.2873
X-RAY DIFFRACTIONr_nbd_other0.2280.26
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21620
X-RAY DIFFRACTIONr_nbtor_other0.2740.210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0230.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3560.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1391.51521
X-RAY DIFFRACTIONr_mcbond_other0.1061.55
X-RAY DIFFRACTIONr_mcangle_it2.04622420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7131040
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1414.5873
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: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 50 -
Rwork0.184 955 -
obs--95.71 %

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