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

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Basic information

Entry
Database: PDB / ID: 5fyp
TitleCalcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, crystal form 2
ComponentsPHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
KeywordsHYDROLASE / PI-PLC / BACTERIAL / PSEUDOMONAS / GRAM-NEGATIVE / CALCIUM-DEPENDENT / APO FORM
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 / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Phosphoinositol-specific phospholipase c
Function and homology information
Biological speciesPSEUDOMONAS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 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: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: 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)132,17618
Polymers131,1014
Non-polymers1,07514
Water33,2021843
1
A: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1826
Polymers32,7751
Non-polymers4065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0765
Polymers32,7751
Non-polymers3004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1045
Polymers32,7751
Non-polymers3284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8152
Polymers32,7751
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.210, 135.210, 112.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPHEPHEAA2 - 2982 - 298
21GLNGLNPHEPHEBB2 - 2982 - 298
12GLNGLNPHEPHEAA2 - 2982 - 298
22GLNGLNPHEPHECC2 - 2982 - 298
13GLNGLNPHEPHEAA2 - 2982 - 298
23GLNGLNPHEPHEDD2 - 2982 - 298
14GLNGLNPROPROBB2 - 2972 - 297
24GLNGLNPROPROCC2 - 2972 - 297
15GLNGLNPROPROBB2 - 2972 - 297
25GLNGLNPROPRODD2 - 2972 - 297
16ALAALAPHEPHECC1 - 2981 - 298
26ALAALAPHEPHEDD1 - 2981 - 298

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 1857 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1843 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.8 % / 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: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.17→67.61 Å / Num. obs: 346088 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FYO

5fyo


Resolution: 1.17→67.61 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.949 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES A 74-77, A 86-90, B 88-90, C 88-90 ARE DISORDERED. DISORDERED REGIONS NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.1476 17243 5 %RANDOM
Rwork0.1248 ---
obs0.12594 328719 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.17→67.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9131 0 56 1843 11030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199814
X-RAY DIFFRACTIONr_bond_other_d0.0090.028873
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.91713325
X-RAY DIFFRACTIONr_angle_other_deg2.153320424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30951265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0124.855484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.188151558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2491542
X-RAY DIFFRACTIONr_chiral_restr0.10.21360
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02111695
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022479
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_it1.7060.9824900
X-RAY DIFFRACTIONr_mcbond_other1.7040.9824897
X-RAY DIFFRACTIONr_mcangle_it1.8721.4776161
X-RAY DIFFRACTIONr_mcangle_other1.8731.4776162
X-RAY DIFFRACTIONr_scbond_it2.7811.1824913
X-RAY DIFFRACTIONr_scbond_other2.7811.1824914
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.16835.6347146
X-RAY DIFFRACTIONr_long_range_B_refined4.85210.88513416
X-RAY DIFFRACTIONr_long_range_B_other4.67913182
X-RAY DIFFRACTIONr_rigid_bond_restr22.483318676
X-RAY DIFFRACTIONr_sphericity_free39.0035337
X-RAY DIFFRACTIONr_sphericity_bonded11.103519878
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A357400.07
12B357400.07
21A352240.09
22C352240.09
31A355340.08
32D355340.08
41B354960.09
42C354960.09
51B352480.09
52D352480.09
61C353780.1
62D353780.1
LS refinement shellResolution: 1.17→1.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 1298 -
Rwork0.209 24067 -
obs--99.79 %

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