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- PDB-3h4x: Structure of a Ca+2 dependent Phosphatidylinositol-specific phosp... -

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Basic information

Entry
Database: PDB / ID: 3h4x
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 / ACETATE ION / ETHANOL / Phosphatidylinositol-specific phospholipase C1
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 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 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Phosphatidylinositol-specific phospholipase C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,35733
Polymers36,7271
Non-polymers1,63032
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.968, 154.819, 41.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphatidylinositol-specific phospholipase C1


Mass: 36726.738 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 expression.
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: plc1, plc1 AB439135.1:1234..2268 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) and B834(DE3)pLysS
References: UniProt: B3A043, phosphoinositide phospholipase C

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Non-polymers , 6 types, 418 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.: 20 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#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: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.65 %
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, 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: 0.82653 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
ReflectionResolution: 1.23→51.99 Å / Num. all: 97853 / Num. obs: 97776 / % possible obs: 99.92 % / Observed criterion σ(I): 3.7 / Redundancy: 7.28 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 8.2141
Reflection shellResolution: 1.23→1.3 Å / Redundancy: 7.11 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3 / Num. measured all: 100339 / Num. unique all: 14115 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.2.25data scaling
REFMACrefmac_5.5.0068refinement
PDB_EXTRACT3.005data extraction
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.23→51.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.183 / Occupancy max: 1 / Occupancy min: 0.45 / SU B: 1.054 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19 9804 10 %RANDOM
Rwork0.173 ---
obs0.174 97776 99.88 %-
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: 50.25 Å2 / Biso mean: 13.796 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.23→51.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 106 386 2903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0212553
X-RAY DIFFRACTIONr_angle_refined_deg0.9881.9543428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4425314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88323.276116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.95915358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5851518
X-RAY DIFFRACTIONr_chiral_restr0.0660.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211975
X-RAY DIFFRACTIONr_mcbond_it0.5451.51603
X-RAY DIFFRACTIONr_mcangle_it0.99422513
X-RAY DIFFRACTIONr_scbond_it1.2913950
X-RAY DIFFRACTIONr_scangle_it2.0324.5915
X-RAY DIFFRACTIONr_rigid_bond_restr0.69532553
X-RAY DIFFRACTIONr_sphericity_free1.5823387
X-RAY DIFFRACTIONr_sphericity_bonded1.74132516
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 (%)
1.23-1.2620.1817590.1736344710499.986
1.262-1.2960.1857180.16362736991100
1.296-1.3340.176880.15961196807100
1.334-1.3750.1796360.15559256561100
1.375-1.420.1746640.15557166380100
1.42-1.470.1726310.14955626193100
1.47-1.5250.1635850.15253945979100
1.525-1.5880.1615680.14951965764100
1.588-1.6580.1645690.14849655534100
1.658-1.7390.1815160.15747825298100
1.739-1.8330.1814930.16445455038100
1.833-1.9440.1864740.16543194793100
1.944-2.0780.1844450.16841024547100
2.078-2.2440.194140.16337624176100
2.244-2.4580.183960.16935123908100
2.458-2.7470.1833270.17632213548100
2.747-3.1710.1993470.17928013148100
3.171-3.880.1812370.1722445269099.703
3.88-5.4720.2022020.1991908213898.69
5.472-51.970.3791350.3271081129493.972

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