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- PDB-5d92: Structure of a phosphatidylinositolphosphate (PIP) synthase from ... -

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Basic information

Entry
Database: PDB / ID: 5d92
TitleStructure of a phosphatidylinositolphosphate (PIP) synthase from Renibacterium Salmoninarum
ComponentsAF2299 protein,Phosphatidylinositol synthase
KeywordsMEMBRANE PROTEIN / Enzyme / lipid biosynthesis / phosphatidylinositol
Function / homology
Function and homology information


phosphotransferase activity, for other substituted phosphate groups / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phospholipid biosynthetic process / nucleotide binding / magnesium ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A - #30 / Phosphatidylinositol phosphate synthase PgsA1 / : / CDP-alcohol phosphatidyltransferase AF_2299-like, N-terminal / CDP-alcohol phosphotransferase transmembrane (TM) domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. ...Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A - #30 / Phosphatidylinositol phosphate synthase PgsA1 / : / CDP-alcohol phosphatidyltransferase AF_2299-like, N-terminal / CDP-alcohol phosphotransferase transmembrane (TM) domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-58A / Octadecane / Phosphatidylinositol phosphate synthase / CDP-alcohol phosphatidyltransferase AF-2299-like N-terminal domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Renibacterium salmoninarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å
AuthorsClarke, O.B. / Tomasek, D.T. / Jorge, C.D. / Belcher Dufrisne, M. / Kim, M. / Banerjee, S. / Rajashankar, K.R. / Hendrickson, W.A. / Santos, H. / Mancia, F.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for phosphatidylinositol-phosphate biosynthesis.
Authors: Clarke, O.B. / Tomasek, D. / Jorge, C.D. / Dufrisne, M.B. / Kim, M. / Banerjee, S. / Rajashankar, K.R. / Shapiro, L. / Hendrickson, W.A. / Santos, H. / Mancia, F.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: AF2299 protein,Phosphatidylinositol synthase
A: AF2299 protein,Phosphatidylinositol synthase
B: AF2299 protein,Phosphatidylinositol synthase
C: AF2299 protein,Phosphatidylinositol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,00949
Polymers150,3914
Non-polymers12,61745
Water00
1
D: AF2299 protein,Phosphatidylinositol synthase
A: AF2299 protein,Phosphatidylinositol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,39528
Polymers75,1962
Non-polymers7,19926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-63 kcal/mol
Surface area33050 Å2
MethodPISA
2
B: AF2299 protein,Phosphatidylinositol synthase
C: AF2299 protein,Phosphatidylinositol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,61421
Polymers75,1962
Non-polymers5,41819
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-62 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.002, 62.489, 169.759
Angle α, β, γ (deg.)90.000, 99.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: -137 - 204 / Label seq-ID: 1 - 342

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAB
2chain BBC
3chain CCD
4chain DDA

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Components

#1: Protein
AF2299 protein,Phosphatidylinositol synthase


Mass: 37597.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea), (gene. exp.) Renibacterium salmoninarum (bacteria)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126, ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
Gene: AF_2299, RSal33209_2010 / Production host: Escherichia coli (E. coli) / References: UniProt: O27985, UniProt: A9WSF5
#2: Chemical...
ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C18H38
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-58A / 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine / cytidinediphosphate-dioleoylglycerol / CDP-1,2-dioleoyl-sn-glycerol


Mass: 1006.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C48H85N3O15P2

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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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30% (v/v) PEG 300, 0.1 M MES pH 6.0, 0.1 M sodium chloride, 0.1 M magnesium chloride (precipitant); Concentrated protein was mixed with molten monoolein in a 1:1.5 (w/w) ratio of protein: ...Details: 30% (v/v) PEG 300, 0.1 M MES pH 6.0, 0.1 M sodium chloride, 0.1 M magnesium chloride (precipitant); Concentrated protein was mixed with molten monoolein in a 1:1.5 (w/w) ratio of protein:lipid using coupled syringes. A Mosquito LCP (TTP Labtech) robot was used to dispense a typical volume of 50-75 nL of protein/lipid mixture onto a 96-well glass sandwich plate, which was covered with 750 nL precipitant solution. Monoolein was doped with 2% CDP-DAG.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.62→166.97 Å / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 79.39 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.15 / Net I/σ(I): 5 / Num. measured all: 78622
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.62-3.973.80.931.41836748780.6160.55297.9
8.87-166.973.60.04219.3544715030.9980.02698.8

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D91

5d91


Resolution: 3.62→166.97 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2997 1043 4.92 %Random selection
Rwork0.2801 20175 --
obs0.2811 21218 98.41 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.71 Å2 / Biso mean: 76.5321 Å2 / Biso min: 26.35 Å2
Refinement stepCycle: final / Resolution: 3.62→166.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10350 0 495 0 10845
Biso mean--63.13 --
Num. residues----1358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01611061
X-RAY DIFFRACTIONf_angle_d1.06814869
X-RAY DIFFRACTIONf_chiral_restr0.0411776
X-RAY DIFFRACTIONf_plane_restr0.0051785
X-RAY DIFFRACTIONf_dihedral_angle_d12.1883944
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6080X-RAY DIFFRACTION8.517TORSIONAL
12B6080X-RAY DIFFRACTION8.517TORSIONAL
13C6080X-RAY DIFFRACTION8.517TORSIONAL
14D6080X-RAY DIFFRACTION8.517TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.613-3.80360.42211690.37642709287895
3.8036-4.04190.29841480.32652888303699
4.0419-4.3540.30971540.29942854300899
4.354-4.79220.3031190.292829363055100
4.7922-5.48560.32331420.2762889303199
5.4856-6.91140.31131520.2922922307499
6.9114-167.47650.22091590.2072977313698

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