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- PDB-5fyr: Calcium-dependent phosphoinositol-specific phospholipase C from a... -

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Basic information

Entry
Database: PDB / ID: 5fyr
TitleCalcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, myoinositol complex
ComponentsPHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
KeywordsHYDROLASE / PI-PLC / BACTERIAL / PSEUDOMONAS / GRAM-NEGATIVE / CALCIUM-DEPENDENT / MYOINOSITOL COMPLEX
Function / homologyPhosphoinositide phospholipase C, Ca2+-dependent / Phosphoinositide phospholipase C, Ca2+-dependent / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / PHOSPHATE ION / Phosphoinositol-specific phospholipase c
Function and homology information
Biological speciesPSEUDOMONAS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMoroz, O.V. / Blagova, E. / Lebedev, A.A. / Norgaard, A. / Segura, D.R. / Blicher, T.H. / Wilson, K.S.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: The structure of a calcium-dependent phosphoinositide-specific phospholipase C from Pseudomonas sp. 62186, the first from a Gram-negative bacterium.
Authors: Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Nrgaard, A. / Segura, D.R. / Blicher, T.H. / Brask, J. / Wilson, K.S.
History
DepositionMar 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
B: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
C: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
D: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,26715
Polymers131,1014
Non-polymers1,16611
Water19,3121072
1
A: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0904
Polymers32,7751
Non-polymers3153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0904
Polymers32,7751
Non-polymers3153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9953
Polymers32,7751
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0904
Polymers32,7751
Non-polymers3153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.443, 135.443, 113.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C


Mass: 32775.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS SP. (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: A0A1S4NYD4*PLUS
#2: Chemical
ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL


Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1072 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.4 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 10
Details: PEG3350 24-27%, CAPS/BICINE MIX PH 9.0-10 GRID, BEST CRYSTALS CLOSER TO PH 10, SEEDING FROM PACT H4 (0.2M KSCN, 20% PEG3350, BIS TRIS PROPANE PH 8.5), ORYX ROBOT, 24 WELL PLATE, HANGING DROPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→48.93 Å / Num. obs: 184175 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FYP

5fyp


Resolution: 1.45→48.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.343 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19184 9159 5 %RANDOM
Rwork0.14488 ---
obs0.14722 174938 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.818 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.45→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9065 0 67 1072 10204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0199582
X-RAY DIFFRACTIONr_bond_other_d0.0020.028649
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.92312977
X-RAY DIFFRACTIONr_angle_other_deg1.101319903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32751202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77424.818467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.608151510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.41540
X-RAY DIFFRACTIONr_chiral_restr0.4680.21338
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111267
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022391
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_it1.8771.4554777
X-RAY DIFFRACTIONr_mcbond_other1.8761.4544775
X-RAY DIFFRACTIONr_mcangle_it2.1452.1885985
X-RAY DIFFRACTIONr_mcangle_other2.1462.1885986
X-RAY DIFFRACTIONr_scbond_it2.7081.6944802
X-RAY DIFFRACTIONr_scbond_other2.7081.6944803
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.21624.8736992
X-RAY DIFFRACTIONr_long_range_B_refined3.96213.39311923
X-RAY DIFFRACTIONr_long_range_B_other3.92513.30611837
X-RAY DIFFRACTIONr_rigid_bond_restr4.143318221
X-RAY DIFFRACTIONr_sphericity_free27.315303
X-RAY DIFFRACTIONr_sphericity_bonded9.027518713
LS refinement shellResolution: 1.453→1.491 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 625 -
Rwork0.167 12609 -
obs--98.07 %

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