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- PDB-9gy2: Non-Hemolytic Phospholipase C (PLC N) -

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Basic information

Entry
Database: PDB / ID: 9gy2
TitleNon-Hemolytic Phospholipase C (PLC N)
Componentsphospholipase C
KeywordsHYDROLASE / Non-Hemolytic / Phospholipase C (PLC N
Function / homology
Function and homology information


phospholipase C / phosphatidylcholine phospholipase C activity / lipid catabolic process
Similarity search - Function
Bacterial phospholipase C, C-terminal domain / Bacterial phospholipase C, phosphocholine-specific / Bacterial phospholipase C, C-terminal domain / Phosphoesterase / Phosphoesterase family / Alkaline-phosphatase-like, core domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsSabharwal, N.S. / Labahn, J.L.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Non-Hemolytic Phospholipase C (PLC N)
Authors: Sabharwal, N.S. / Labahn, J.L.
History
DepositionOct 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phospholipase C
B: phospholipase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9316
Polymers157,7712
Non-polymers1604
Water21,2221178
1
A: phospholipase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9663
Polymers78,8851
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: phospholipase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9663
Polymers78,8851
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.270, 110.432, 98.619
Angle α, β, γ (deg.)90.000, 101.030, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein phospholipase C


Mass: 78885.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 6HisTag at the N terminal of full length PLC N (non-hemolytic phospholipase C)
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: plcN, PA14_21110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2ZE19, phospholipase C
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: 11% 1,5-pentadiol, 0.1 M BisTris/MOPSO pH 6.5, 7% PEG 8000. With 1:1200 trypsin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.57→47.96 Å / Num. obs: 170135 / % possible obs: 95 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.23 Å2 / CC1/2: 1 / Net I/σ(I): 20.2
Reflection shellResolution: 1.57→1.59 Å / Num. unique obs: 5609 / CC1/2: 0.847

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→47.96 Å / SU ML: 0.1568 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1754 8504 5 %
Rwork0.152 161631 -
obs0.1532 170135 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.88 Å2
Refinement stepCycle: LAST / Resolution: 1.57→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10211 0 4 1178 11393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007810538
X-RAY DIFFRACTIONf_angle_d0.987714349
X-RAY DIFFRACTIONf_chiral_restr0.05881468
X-RAY DIFFRACTIONf_plane_restr0.0131915
X-RAY DIFFRACTIONf_dihedral_angle_d13.81713863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.29032670.24595348X-RAY DIFFRACTION94.9
1.63-1.650.24942930.20485389X-RAY DIFFRACTION94.81
1.65-1.670.22952720.1945301X-RAY DIFFRACTION94.71
1.67-1.690.21112800.1925326X-RAY DIFFRACTION94.3
1.69-1.720.25353060.21515286X-RAY DIFFRACTION93.46
1.72-1.740.23572800.21685174X-RAY DIFFRACTION91.3
1.74-1.770.21242600.20134690X-RAY DIFFRACTION83.71
1.77-1.80.21282540.17635448X-RAY DIFFRACTION95.26
1.8-1.830.18883180.16545417X-RAY DIFFRACTION96.39
1.83-1.860.19372900.16015462X-RAY DIFFRACTION96.35
1.86-1.90.17412950.155429X-RAY DIFFRACTION96.4
1.9-1.940.17733100.14775434X-RAY DIFFRACTION96.26
1.94-1.980.19212890.15355445X-RAY DIFFRACTION96.5
1.98-2.020.1972850.15535471X-RAY DIFFRACTION96.66
2.02-2.070.17872960.15845458X-RAY DIFFRACTION96.58
2.07-2.130.16192700.15375469X-RAY DIFFRACTION96.34
2.13-2.190.17943040.1445505X-RAY DIFFRACTION96.58
2.19-2.260.17572630.14195466X-RAY DIFFRACTION96.12
2.26-2.350.16572880.1435386X-RAY DIFFRACTION94.98
2.35-2.440.1762580.154983X-RAY DIFFRACTION88.13
2.44-2.550.16392870.14545267X-RAY DIFFRACTION92.85
2.55-2.680.1692770.14515594X-RAY DIFFRACTION97.95
2.68-2.850.17022980.15225532X-RAY DIFFRACTION98.08
2.85-3.070.1612740.14785624X-RAY DIFFRACTION98.07
3.07-3.380.15672760.14415575X-RAY DIFFRACTION97.91
3.38-3.870.16812770.13645550X-RAY DIFFRACTION97.25
3.87-4.880.14432780.13165113X-RAY DIFFRACTION89.34
4.88-47.960.182840.15425774X-RAY DIFFRACTION99.25

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