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- PDB-7cne: Crystal Structure of Sphingomyelinase C from Streptomyces griseoc... -

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Basic information

Entry
Database: PDB / ID: 7cne
TitleCrystal Structure of Sphingomyelinase C from Streptomyces griseocarneus
ComponentsSphingomyelinase C
KeywordsHYDROLASE / Sphingomyelinase C / Streptomyces griseocarneus / Metal-binding site
Function / homology
Function and homology information


sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / extracellular region
Similarity search - Function
Sphingomyelinase C/phospholipase C / Sphingomyelin phosphodiesterase 2-like / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
SUCCINIC ACID / Sphingomyelinase C
Similarity search - Component
Biological speciesStreptomyces griseocarneus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMurayama, K. / Fujisawa, I. / Sugimori, D.
CitationJournal: J.Biosci.Bioeng. / Year: 2021
Title: Structural basis for the high thermal stability and optimum pH of sphingomyelinase C from Streptomyces griseocarneus.
Authors: Fujisawa, I. / Hamana, H. / Tomita, Y. / Matsumoto, Y. / Murayama, K. / Sugimori, D.
History
DepositionJul 31, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 28, 2020ID: 3WCX
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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
A: Sphingomyelinase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5733
Polymers32,2161
Non-polymers3562
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint0 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.091, 66.091, 142.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Sphingomyelinase C


Mass: 32216.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseocarneus (bacteria) / Gene: smc / Production host: Streptomyces lividans (bacteria)
References: UniProt: A6P7M9, sphingomyelin phosphodiesterase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.95M succinic acid, 1% PEGMME 2000, 0.1M HEPES buffer pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→48.5 Å / Num. obs: 22156 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 24.02 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 36.6
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 2162 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZWX

1zwx


Resolution: 2→48.45 Å / SU ML: 0.1672 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0148 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.201 2000 9.06 %
Rwork0.1626 20087 -
obs0.1662 22087 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.51 Å2
Refinement stepCycle: LAST / Resolution: 2→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 23 303 2569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642332
X-RAY DIFFRACTIONf_angle_d0.80273181
X-RAY DIFFRACTIONf_chiral_restr0.0554331
X-RAY DIFFRACTIONf_plane_restr0.005423
X-RAY DIFFRACTIONf_dihedral_angle_d4.09541827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2371380.16671389X-RAY DIFFRACTION99.16
2.05-2.110.22471390.16471395X-RAY DIFFRACTION100
2.11-2.170.23591390.16381391X-RAY DIFFRACTION99.93
2.17-2.240.22051410.16421420X-RAY DIFFRACTION100
2.24-2.320.21711390.1561393X-RAY DIFFRACTION100
2.32-2.410.19271420.16241421X-RAY DIFFRACTION100
2.41-2.520.26491400.17441422X-RAY DIFFRACTION100
2.52-2.650.19681420.17221421X-RAY DIFFRACTION100
2.65-2.820.2361410.17991416X-RAY DIFFRACTION100
2.82-3.040.23451430.18471442X-RAY DIFFRACTION100
3.04-3.340.2171450.17831453X-RAY DIFFRACTION100
3.34-3.830.18251450.14411448X-RAY DIFFRACTION100
3.83-4.820.14641470.1321478X-RAY DIFFRACTION100
4.82-48.450.18531590.17231598X-RAY DIFFRACTION100

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