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- PDB-9bcz: Chicken 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase... -

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Basic information

Entry
Database: PDB / ID: 9bcz
TitleChicken 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta-1 (PLCZ1) in complex with calcium and phosphorylated threonine
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta-1
KeywordsHYDROLASE / Phospholipase-C / lipid-metabolism / calcium-binding / oocyte-activation / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of cytosolic calcium ion concentration involved in egg activation / Synthesis of IP3 and IP4 in the cytosol / phosphoinositide phospholipase C / sperm head / phosphatidylinositol-5-phosphate binding / phosphatidylinositol phospholipase C activity / phosphatidylinositol-3-phosphate binding / pronucleus / lipid catabolic process / phosphatidylinositol-4,5-bisphosphate binding ...positive regulation of cytosolic calcium ion concentration involved in egg activation / Synthesis of IP3 and IP4 in the cytosol / phosphoinositide phospholipase C / sperm head / phosphatidylinositol-5-phosphate binding / phosphatidylinositol phospholipase C activity / phosphatidylinositol-3-phosphate binding / pronucleus / lipid catabolic process / phosphatidylinositol-4,5-bisphosphate binding / calcium ion transport / intracellular signal transduction / nucleolus / perinuclear region of cytoplasm / nucleoplasm / nucleus
Similarity search - Function
Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X ...Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / EF-hand domain pair
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsEdwards, M.M. / Dong, A. / Theo-Emegano, N. / Seitova, A. / Loppnau, P. / Leung, R. / Li, H. / Ilyassov, O. / Edwards, A.M. / Arrowsmith, C.H. ...Edwards, M.M. / Dong, A. / Theo-Emegano, N. / Seitova, A. / Loppnau, P. / Leung, R. / Li, H. / Ilyassov, O. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-033527 United States
CitationJournal: To be published
Title: Chicken 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta-1 (PLCZ1) in complex with calcium and phosphorylated threonine
Authors: Edwards, M.M. / Dong, A. / Theo-Emegano, N. / Seitova, A. / Loppnau, P. / Leung, R. / Li, H. / Ilyassov, O. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium
History
DepositionApr 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,35114
Polymers73,6611
Non-polymers69113
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, Size exclusion chromatography Multi-angle light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.182, 85.539, 98.433
Angle α, β, γ (deg.)90.00, 112.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta-1 / Phosphoinositide phospholipase C-zeta-1 / Phospholipase C-zeta-1 / PLC-zeta-1


Mass: 73660.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: PLCZ1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q2VRL0, phosphoinositide phospholipase C

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Non-polymers , 7 types, 169 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.2962.6
265735
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M NaHEPES, MOPs acidic pH 7.5, 20% PEG 550 MME & 10% PEG 20,000, 0.2 M Monosaccharides

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95307 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95307 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 60478 / % possible obs: 94.7 % / Redundancy: 6 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.07 / Rrim(I) all: 0.178 / Χ2: 1.072 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.034.30.92724090.6630.8930.4431.0310.79175.8
2.03-2.074.60.85725210.7160.9130.3960.9470.8478.2
2.07-2.114.90.8325450.750.9260.3740.9130.8581.3
2.11-2.155.10.73126910.8020.9440.3220.8010.86684.9
2.15-2.25.30.65428340.8520.9590.2840.7150.87588.5
2.2-2.255.50.62829680.8690.9640.2690.6850.88493.1
2.25-2.315.70.55730300.8960.9720.2390.6080.87196
2.31-2.375.80.4931060.9190.9790.210.5340.87898.1
2.37-2.445.90.45731600.9270.9810.20.50.89299.2
2.44-2.525.80.40731870.9270.9810.1840.4480.89199.7
2.52-2.616.50.34431750.9610.990.1460.3740.9499.7
2.61-2.716.30.331610.9630.990.130.3280.95399.7
2.71-2.846.70.25231800.9720.9930.1060.2730.99599.7
2.84-2.997.10.20532210.9850.9960.0820.2211.02999.9
2.99-3.177.10.16831620.9870.9970.0680.1811.16299.9
3.17-3.426.90.1332150.9910.9980.0530.1411.283100
3.42-3.766.80.10232000.9930.9980.0420.111.453100
3.76-4.316.40.07832160.9950.9990.0330.0851.513100
4.31-5.435.60.06432210.9940.9990.030.0711.43399.9
5.43-506.70.05832760.9970.9990.0240.0631.38299.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→49.59 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.784 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20412 2998 5 %RANDOM
Rwork0.17287 ---
obs0.17439 57477 94.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.353 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å2-1.91 Å2
2---1.77 Å2-0 Å2
3---2.75 Å2
Refinement stepCycle: 1 / Resolution: 1.99→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 45 156 5019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125063
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164713
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6576860
X-RAY DIFFRACTIONr_angle_other_deg0.5071.57410889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.501525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47510857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021182
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7482.7312466
X-RAY DIFFRACTIONr_mcbond_other2.7362.7312466
X-RAY DIFFRACTIONr_mcangle_it4.0784.8983091
X-RAY DIFFRACTIONr_mcangle_other4.0784.93092
X-RAY DIFFRACTIONr_scbond_it3.8753.132597
X-RAY DIFFRACTIONr_scbond_other3.8593.1282595
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other65.5313758
X-RAY DIFFRACTIONr_long_range_B_refined7.6727.195556
X-RAY DIFFRACTIONr_long_range_B_other7.65127.185529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.992→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 155 -
Rwork0.264 3039 -
obs--67.77 %

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