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- PDB-6wm5: Structure of a phosphatidylinositol-phosphate synthase (PIPS) fro... -

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Basic information

Entry
Database: PDB / ID: 6wm5
TitleStructure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii
ComponentsAfCTD-Phosphatidylinositol-phosphate synthase (PIPS) fusion
KeywordsMEMBRANE PROTEIN / CDP-alcohol phosphotransferase / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phosphotransferase activity, for other substituted phosphate groups / phospholipid biosynthetic process / nucleotide binding / magnesium ion binding / metal ion binding / membrane / 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
Octadecane / CITRATE ANION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / 3,3',3''-phosphanetriyltripropanoic acid / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / CDP-alcohol phosphatidyltransferase AF-2299-like N-terminal domain-containing protein / CDP-alcohol phosphatidyltransferase AF-2299-like N-terminal domain-containing protein / Phosphatidylinositol phosphate synthase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Mycobacterium kansasii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.961 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. / New York Consortium on Membrane Protein Structure (NYCOMPS)
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 20, 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)91,76652
Polymers80,7782
Non-polymers10,98950
Water1,856103
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 area9190 Å2
ΔGint-117 kcal/mol
Surface area31360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.338, 60.241, 85.377
Angle α, β, γ (deg.)90.000, 90.910, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -137 through -126 or resid -124...
21(chain C and (resid -137 through -126 or resid -124...

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
11LEULEUGLUGLU(chain A and (resid -137 through -126 or resid -124...AA-137 - -1263 - 14
12LEULEULEULEU(chain A and (resid -137 through -126 or resid -124...AA-124 - -11916 - 21
13GLUGLUALAALA(chain A and (resid -137 through -126 or resid -124...AA-117 - -9323 - 47
14GLUGLUGLUGLU(chain A and (resid -137 through -126 or resid -124...AA-9248
15METMETILEILE(chain A and (resid -137 through -126 or resid -124...AA-139 - 2091 - 347
16METMETILEILE(chain A and (resid -137 through -126 or resid -124...AA-139 - 2091 - 347
17METMETILEILE(chain A and (resid -137 through -126 or resid -124...AA-139 - 2091 - 347
18METMETILEILE(chain A and (resid -137 through -126 or resid -124...AA-139 - 2091 - 347
21LEULEUGLUGLU(chain C and (resid -137 through -126 or resid -124...CB-137 - -1263 - 14
22LEULEULEULEU(chain C and (resid -137 through -126 or resid -124...CB-124 - -11916 - 21
23GLUGLUGLUGLU(chain C and (resid -137 through -126 or resid -124...CB-11723
24METMETPROPRO(chain C and (resid -137 through -126 or resid -124...CB-139 - 2101 - 348
25METMETPROPRO(chain C and (resid -137 through -126 or resid -124...CB-139 - 2101 - 348
26METMETPROPRO(chain C and (resid -137 through -126 or resid -124...CB-139 - 2101 - 348
27METMETPROPRO(chain C and (resid -137 through -126 or resid -124...CB-139 - 2101 - 348

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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 (bacteria)
Gene: XD40_0003, XD48_0797, MKAN_RS24880 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A101DFK9, UniProt: U5WZP7, UniProt: O27985*PLUS

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Non-polymers , 9 types, 153 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


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


Mass: 254.494 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C18H38
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-XP4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 591.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H60O8P / Comment: DMPA, phospholipid*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6
Details: 100 mM Sodium citrate, pH 6, 50 mM sodium chloride, 20 mM magnesium chloride hexahydrate, 22% PEG 400 (precipitant). Concentrated protein at 30-35 mg/ml was mixed with monoolein (Sigma) in a ...Details: 100 mM Sodium citrate, pH 6, 50 mM sodium chloride, 20 mM magnesium chloride hexahydrate, 22% PEG 400 (precipitant). Concentrated protein at 30-35 mg/ml was mixed with monoolein (Sigma) in a 1:1.5 protein to lipid ratio (w/w). Monoolein was doped with 2% CDP-DAG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2017 / Details: MD2 diffractometer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.96→49.22 Å / Num. obs: 37482 / % possible obs: 66 % / Redundancy: 1.9 % / Biso Wilson estimate: 25.57 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.1061 / Rpim(I) all: 0.1061 / Rrim(I) all: 0.1501 / Net I/σ(I): 6.23
Reflection shellResolution: 1.96→2.037 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 183 / CC1/2: 0.11 / CC star: 0.445 / Rpim(I) all: 0.64 / Rrim(I) all: 0.9051 / % possible all: 3.27

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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: 1.961→49.22 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.2
RfactorNum. reflection% reflection
Rfree0.277 1930 5.15 %
Rwork0.2347 --
obs0.2369 37478 65.38 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 85.51 Å2 / Biso mean: 33.7529 Å2 / Biso min: 4.04 Å2
Refinement stepCycle: final / Resolution: 1.961→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5025 0 460 103 5588
Biso mean--38.6 35.78 -
Num. residues----672
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2806X-RAY DIFFRACTION14.015TORSIONAL
12C2806X-RAY DIFFRACTION14.015TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.961-2.010.424550.4274682
2.01-2.06430.201140.41312988
2.0643-2.12510.4709360.361566217
2.1251-2.19370.3763610.3491116430
2.1937-2.27210.3412940.327167143
2.2721-2.36310.36341100.3114220457
2.3631-2.47060.35481560.2911303079
2.4706-2.60090.34862060.2753357292
2.6009-2.76380.30851690.2645376396
2.7638-2.97720.28321980.2545382698
2.9772-3.27670.28021880.251382598
3.2767-3.75070.26422080.2225382798
3.7507-4.72490.23662310.1796379598
4.7249-49.220.24152540.1975384397

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