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- PDB-6wmv: Structure of a phosphatidylinositol-phosphate synthase (PIPS) fro... -

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Basic information

Entry
Database: PDB / ID: 6wmv
TitleStructure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii with evidence of substrate binding
ComponentsAfCTD-Phosphatidylinositol-phosphate synthase (PIPS) fusion
KeywordsMEMBRANE PROTEIN / CDP-alcohol phosphotransferase
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
Phosphatidylinositol phosphate synthase PgsA1 / : / CDP-alcohol phosphatidyltransferase AF_2299-like, N-terminal / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature.
Similarity search - Domain/homology
Octadecane / CYTIDINE-5'-MONOPHOSPHATE / CITRATE ANION / L-MYO-INOSITOL-1-PHOSPHATE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 3,3',3''-phosphanetriyltripropanoic acid / CDP-alcohol phosphatidyltransferase family protein / CDP-alcohol phosphatidyltransferase AF-2299-like N-terminal domain-containing protein / Phosphatidylinositol phosphate synthase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Mycobacterium kansasii ATCC 12478 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.142 Å
AuthorsBelcher Dufrisne, M. / Jorge, C.D. / Timoteo, C.G. / Petrou, V.I. / Ashraf, K.U. / Banerjee, S. / Clarke, O.B. / Santos, H. / Mancia, F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI119672 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM132120 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM111980 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural and Functional Characterization of Phosphatidylinositol-Phosphate Biosynthesis in Mycobacteria.
Authors: Belcher Dufrisne, M. / Jorge, C.D. / Timoteo, C.G. / Petrou, V.I. / Ashraf, K.U. / Banerjee, S. / Clarke, O.B. / Santos, H. / Mancia, F.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.classification / _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
A: AfCTD-Phosphatidylinositol-phosphate synthase (PIPS) fusion
C: AfCTD-Phosphatidylinositol-phosphate synthase (PIPS) fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,66628
Polymers80,7782
Non-polymers5,88826
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, PIPS from Mycobacterium kansasii crystallizes as a dimer as other PIPS enzymes from Renibacterium salmoninarum (PDB 5D91 and 5D92) and Mycobacterium tuberculosis (PDB 6H53, 6H5A, ...Evidence: homology, PIPS from Mycobacterium kansasii crystallizes as a dimer as other PIPS enzymes from Renibacterium salmoninarum (PDB 5D91 and 5D92) and Mycobacterium tuberculosis (PDB 6H53, 6H5A, 6H59) as well as other members of the CDP-alcohol phosphotransferase family such as IPCT-DIPPS (PDB 4MND) and Af2299 (PDB 4Q7C, 4O6M, 4O6N).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-85 kcal/mol
Surface area30410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.089, 60.857, 85.417
Angle α, β, γ (deg.)90.000, 90.740, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid -139 and (name N or name...
21(chain C and (resid -139 through -126 or (resid -125...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain A and ((resid -139 and (name N or name...AA-1391
12METMETILEILE(chain A and ((resid -139 and (name N or name...AA-139 - 2091 - 347
13METMETILEILE(chain A and ((resid -139 and (name N or name...AA-139 - 2091 - 347
14METMETILEILE(chain A and ((resid -139 and (name N or name...AA-139 - 2091 - 347
15METMETILEILE(chain A and ((resid -139 and (name N or name...AA-139 - 2091 - 347
21METMETGLUGLU(chain C and (resid -139 through -126 or (resid -125...CB-139 - -1261 - 14
22LYSLYSLYSLYS(chain C and (resid -139 through -126 or (resid -125...CB-12515

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein AfCTD-Phosphatidylinositol-phosphate synthase (PIPS) fusion


Mass: 40388.797 Da / Num. of mol.: 2 / Mutation: D17L,Q77L,G79S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea), (gene. exp.) Mycobacterium kansasii ATCC 12478 (bacteria)
Gene: XD40_0003, XD48_0797, MKAN_26045 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A101DFK9, UniProt: U5WZP7, UniProt: O27985*PLUS

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Non-polymers , 10 types, 53 molecules

#2: Chemical ChemComp-LIP / L-MYO-INOSITOL-1-PHOSPHATE


Mass: 258.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical
ChemComp-8K6 / Octadecane / N-Octadecane / Octadecane


Mass: 254.494 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H38
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6.1
Details: 100 mM NaCl, 100 mM Sodium Citrate, pH 6.1, 40 mM MgCl2, 29% PEG 400, 500 uM L-myo-inositol-1-phosphate (prepared in house), 2.5 mM CDP (Sigma) (precipitant). Concentrated protein at 30-35 ...Details: 100 mM NaCl, 100 mM Sodium Citrate, pH 6.1, 40 mM MgCl2, 29% PEG 400, 500 uM L-myo-inositol-1-phosphate (prepared in house), 2.5 mM CDP (Sigma) (precipitant). Concentrated protein at 30-35 mg/ml was mixed with monoolein at a 1:1.5 protein to lipid ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2018 / Details: MD2 diffractometer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.142→78.083 Å / Num. obs: 26006 / % possible obs: 58.72 % / Redundancy: 2 % / Biso Wilson estimate: 41.06 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.07329 / Rpim(I) all: 0.07329 / Rrim(I) all: 0.1036 / Net I/σ(I): 9.78
Reflection shellResolution: 2.142→2.221 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4034 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 69 / CC1/2: 0.594 / CC star: 0.863 / Rpim(I) all: 0.4034 / Rrim(I) all: 0.5705 / % possible all: 1.57

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
STARANISOdata scaling
PARROTphasing
PHENIX1.13_2998refinement
Cootmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D91,4O6M

5d91

4o6m


Resolution: 2.142→78.083 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 36.47
RfactorNum. reflection% reflection
Rfree0.2695 1297 4.99 %
Rwork0.2228 --
obs0.2252 25995 58.53 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 116.15 Å2 / Biso mean: 45.381 Å2 / Biso min: 13.24 Å2
Refinement stepCycle: final / Resolution: 2.142→78.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5013 0 268 27 5308
Biso mean--54.22 39.3 -
Num. residues----672
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2871X-RAY DIFFRACTION11.366TORSIONAL
12C2871X-RAY DIFFRACTION11.366TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.142-2.22760.52930.2952842
2.2276-2.3290.6081230.28445910
2.329-2.45180.3598630.310293920
2.4518-2.60540.3141920.3008212845
2.6054-2.80650.32721670.2824310267
2.8065-3.0890.29242260.2905387983
3.089-3.5360.31042120.2475463598
3.536-4.45490.26472360.19394699100
4.4549-78.080.22732750.1916477399

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