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- PDB-1zwx: Crystal Structure of SmcL -

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Basic information

Entry
Database: PDB / ID: 1zwx
TitleCrystal Structure of SmcL
Componentssphingomyelinase-c
KeywordsHYDROLASE / DNase1-like fold / beta-hairpin
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
PHOSPHATE ION / Sphingomyelinase C
Similarity search - Component
Biological speciesListeria ivanovii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsOpenshaw, A.E.A. / Race, P.R. / Monzo, H.J. / Vasquez-Boland, J.A. / Banfield, M.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of SmcL, a bacterial neutral sphingomyelinase C from Listeria.
Authors: Openshaw, A.E.A. / Race, P.R. / Monzo, H.J. / Vasquez-Boland, J.A. / Banfield, M.J.
History
DepositionJun 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE This is an error in the protein sequence database. The sequence of the deposited structure ...SEQUENCE This is an error in the protein sequence database. The sequence of the deposited structure agrees with recent, repeated DNA sequencing of the locus in the parent organism.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sphingomyelinase-c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6903
Polymers34,5021
Non-polymers1872
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: sphingomyelinase-c
hetero molecules

A: sphingomyelinase-c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3796
Polymers69,0052
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3580 Å2
ΔGint-34 kcal/mol
Surface area22570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.860, 66.860, 180.848
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein sphingomyelinase-c / SmcL


Mass: 34502.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria ivanovii (bacteria) / Gene: smcl / Plasmid: pET27b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q9RLV9, sphingomyelin phosphodiesterase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 3.4 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 8000, sodium citrate, sodium dihydrogen phosphate, sodium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 5, 2005 / Details: Mirrors
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
Reflection
Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsRsym valueD res high (Å)D res low (Å)% possible obs
3.819.4152680.0670.0672.5955.5699.3
8.329.598740.0750.075332.7899.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.2255.5699.210.0260.0263.4
5.818.2210010.0390.0393.9
4.755.8110010.0410.0414
4.114.7510010.0480.0484.1
3.684.1110010.0640.0644.1
3.363.6810010.0750.0754.1
3.113.3610010.0910.0914.1
2.913.1110010.1450.1454.1
2.742.919910.150.153.7
2.62.7496.110.1740.1742.4
9.4932.7897.820.020.026.5
6.719.4910020.0280.0287.8
5.486.7110020.050.058.1
4.745.4810020.0370.0378.3
4.244.7410020.0410.0418.4
3.874.2410020.0590.0598.4
3.593.8710020.0890.0898.4
3.353.5910020.1240.1248.4
3.163.3510020.1820.1828.5
33.1610020.2610.2618.4
ReflectionResolution: 1.9→30.68 Å / Num. obs: 37481 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 18.8
Reflection shellResolution: 1.9→2 Å / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 5409 / Num. unique all: 5409 / Rsym value: 0.263 / % possible all: 100

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Phasing

PhasingMethod: SIRAS
Phasing dmFOM : 0.68 / FOM acentric: 0.67 / FOM centric: 0.76 / Reflection: 13795 / Reflection acentric: 11804 / Reflection centric: 1991
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-35.7060.890.90.86712455257
4.6-7.40.860.870.8320581631427
3.7-4.60.850.840.8524912103388
3.3-3.70.780.770.8124722159313
2.8-3.30.570.560.6540293599430
2.6-2.80.350.330.4620331857176
Phasing MIRResolution: 3→40 Å / FOM: 0.31 / Reflection: 9681
Phasing MIR der
IDDer set-ID
11
21
31
41
Phasing MIR der site

ID: 1 / Atom type symbol: Ir

Der-IDBiso (Å)Fract xFract yFract zOccupancy
152.24110.26460.54750.03820.4134
221.1490.95440.28210.04970.065
36.9890.05460.84360.01320.0445
422.98280.34590.76660.15640.048
Phasing MIR shell
Resolution (Å)FOMReflection
10.7-400.53511
6.79-10.70.55845
5.32-6.790.471040
4.51-5.320.361218
3.99-4.510.291371
3.61-3.990.231486
3.32-3.610.211565
3.1-3.320.171645

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefinement
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→30.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.919 / SU ML: 0.086 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.124 / ESU R Free: 0.121 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1888 5 %RANDOM
Rwork0.201 ---
obs0.203 35586 100 %-
all-37475 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.572 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20.9 Å20 Å2
2--1.8 Å20 Å2
3----2.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.121 Å0.124 Å
Refinement stepCycle: LAST / Resolution: 1.9→30.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 11 244 2556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212401
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9143259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75224.426122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89715383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8231510
X-RAY DIFFRACTIONr_chiral_restr0.110.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021867
X-RAY DIFFRACTIONr_nbd_refined0.1920.21095
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.211
X-RAY DIFFRACTIONr_mcbond_it0.9811.51470
X-RAY DIFFRACTIONr_mcangle_it1.63622319
X-RAY DIFFRACTIONr_scbond_it2.39231080
X-RAY DIFFRACTIONr_scangle_it3.5964.5940
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 145 -
Rwork0.254 2554 -
obs-35586 100 %

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