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- PDB-3h4w: Structure of a Ca+2 dependent Phosphatidylinositol-specific phosp... -

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Basic information

Entry
Database: PDB / ID: 3h4w
TitleStructure of a Ca+2 dependent Phosphatidylinositol-specific phospholipase C (PI-PLC) Enzyme from Streptomyces antibioticus
ComponentsPhosphatidylinositol-specific phospholipase C1
KeywordsHYDROLASE / PI-PLC / Ca2+-dependent / catalytic TIM barrel / disulfide-linked helix-loop
Function / homology
Function and homology information


phosphoinositide phospholipase C / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / lipid metabolic process
Similarity search - Function
Phosphoinositide phospholipase C, Ca2+-dependent / Phosphoinositide phospholipase C, Ca2+-dependent / Phosphatidylinositol (PI) phosphodiesterase / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / ETHANOL / Phosphatidylinositol-specific phospholipase C1
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJackson, M.R. / Selby, T.L.
CitationJournal: To be Published
Title: Crystal Structure of a Ca2+-dependent PI-PLC
Authors: Jackson, M.R. / Selby, T.L.
History
DepositionApr 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol-specific phospholipase C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,63615
Polymers36,8671
Non-polymers76814
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.377, 155.172, 41.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphatidylinositol-specific phospholipase C1


Mass: 36867.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal aa sequence in the gene (1.mngkrcvgtasraaaaviavsgpaga.26) is cleaved off by the organism and was replaced with the HIS-tagged sequence (1.MGSSHHHHHHSSGLVPRGSHM.21) for protein ...Details: The N-terminal aa sequence in the gene (1.mngkrcvgtasraaaaviavsgpaga.26) is cleaved off by the organism and was replaced with the HIS-tagged sequence (1.MGSSHHHHHHSSGLVPRGSHM.21) for protein expression. Selenomethionine incorporation using auxotrophic strain and synthetically substituted media.
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: plc1, plc1 AB439135.1:1234..2268 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS
References: UniProt: B3A043, phosphoinositide phospholipase C

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Non-polymers , 5 types, 328 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE RESIDUE 264 IN COORDINATES IS OBSERVED AS ALA, WHERE IT IS LISTED AS PRO IN UNP.

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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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 21% PEG 10000, 85mM sodium acetate pH 4.6, 170mM ammonium acetate, 9% glycerol. SeMe-derived crystals obtained with initial microseeding with underivatized crystals followed by a series of ...Details: 21% PEG 10000, 85mM sodium acetate pH 4.6, 170mM ammonium acetate, 9% glycerol. SeMe-derived crystals obtained with initial microseeding with underivatized crystals followed by a series of macroseedings with derivatized enzyme and same conditions., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.5→77.61 Å / Num. all: 52173 / Num. obs: 52171 / % possible obs: 95.15 % / Observed criterion σ(I): 3.7 / Redundancy: 11.65 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.2689
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.76 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.19 / Num. measured all: 36537 / Num. unique all: 6345 / % possible all: 81.66

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
112.39731.3880.448S201
222.1959.6074.931S200.88
312.69731.592-6.665S200.659
44.55522.236-6.836S200.421
5-12.1318.215-0.899S200.1
614.41916.9118.371S200.091
712.67933.157-14.943S200.089
81.2072.2368.918S200.085
9-12.28811.35814.31S200.053
10-14.72511.31620.55S200.046
114.11544.8736.667S200.031

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.2.25data scaling
SHELXphasing
REFMACrefmac_5.5.0068refinement
PDB_EXTRACT3.005data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→77.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.192 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.281 / SU ML: 0.04 / ESU R: 0.103 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOO
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2 5234 10 %RANDOM
Rwork0.184 ---
obs0.185 52168 94.73 %-
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 max: 54.16 Å2 / Biso mean: 14.295 Å2 / Biso min: 6.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---0.61 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→77.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 49 314 2774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212515
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.9463406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1115314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27523.276116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.88315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8591518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211963
X-RAY DIFFRACTIONr_mcbond_it0.5671.51576
X-RAY DIFFRACTIONr_mcangle_it0.98122492
X-RAY DIFFRACTIONr_scbond_it1.5913939
X-RAY DIFFRACTIONr_scangle_it2.194.5914
X-RAY DIFFRACTIONr_rigid_bond_restr0.87732515
X-RAY DIFFRACTIONr_sphericity_free2.3443315
X-RAY DIFFRACTIONr_sphericity_bonded1.67432459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.2053090.1722655401273.878
1.54-1.5820.2013420.1613020391985.787
1.582-1.6280.1853540.1493138380191.871
1.628-1.6780.1843650.1513192366797
1.678-1.7330.1993700.1563176359098.774
1.733-1.7940.2073270.1613129348199.282
1.794-1.8620.2153370.1642997335499.404
1.862-1.9380.2112690.1862614323689.091
1.938-2.0240.2033050.1782800311599.679
2.024-2.1220.1933060.1762639294999.864
2.122-2.2370.1812800.1752513285797.76
2.237-2.3730.2212150.182252269691.506
2.373-2.5360.1682770.17122642541100
2.536-2.7390.1992310.1821602391100
2.739-30.1972100.18319752185100
3-3.3540.1922200.18317751995100
3.354-3.8710.1871660.1791507179293.359
3.871-4.7390.171680.18613631531100
4.739-6.6890.2411180.24311021220100
6.689-77.590.368650.35566373898.645

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