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- PDB-6h5a: Crystal structure of Mycobacterium tuberculosis phosphatidylinosi... -

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Basic information

Entry
Database: PDB / ID: 6h5a
TitleCrystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) in complex with manganese and citrate
ComponentsCDP-diacylglycerol--inositol 3-phosphatidyltransferase
KeywordsTRANSFERASE / Phosphotransferase Glycerophospholipid metabolism Metal binding protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity / glycerophospholipid biosynthetic process / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phospholipid biosynthetic process / peptidoglycan-based cell wall / magnesium ion binding / plasma membrane
Similarity search - Function
Phosphatidylinositol phosphate synthase PgsA1 / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature.
Similarity search - Domain/homology
CITRATE ANION / EICOSANE / : / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Phosphatidylinositol phosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsGrave, K. / Hogbom, M.
CitationJournal: Commun Biol / Year: 2019
Title: Structure ofMycobacterium tuberculosisphosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis.
Authors: Grave, K. / Bennett, M.D. / Hogbom, M.
History
DepositionJul 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDP-diacylglycerol--inositol 3-phosphatidyltransferase
B: CDP-diacylglycerol--inositol 3-phosphatidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,86322
Polymers48,1392
Non-polymers3,72420
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-92 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.067, 77.941, 100.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CDP-diacylglycerol--inositol 3-phosphatidyltransferase / Phosphatidylinositol synthase / PI synthase


Mass: 24069.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residue fragment 218-223 in chain B (-ENLYFQ) is a remnant after cloning/protease cleavage.
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pgsA1, Rv2612c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rossetta2 / References: UniProt: P9WPG7, EC: 2.7.8.11

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Non-polymers , 7 types, 146 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H42
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: 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
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6
Details: 31% PEG 400 (v/v), 0.1 M NaCl, 0.12 M MnCl2 and 0.1 M trisodium citrate dihydrate pH 6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06SA21.88
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELMay 29, 2016
DECTRIS EIGER X 16M2PIXELMay 29, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.881
Reflection

Biso Wilson estimate: 24.91 Å2 / Entry-ID: 6H5A

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/av σ(I)Net I/σ(I)
1.88-45.6994395698.876.80.9990.14270.05870.154614.59.52
3.19-45.79934998.9813.20.0960.02710.0997222.55
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
1.88-1.9512.81.0631.4642810.4090.4391.152197.92
3.19-3.1913.60.215610.939220.9990.05960.2238299.68

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H53

6h53


Resolution: 1.88→45.699 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.57
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 2198 5 %Random selection
Rwork0.2037 ---
obs0.2051 43956 98.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.45 Å2 / Biso mean: 30.44 Å2 / Biso min: 14.24 Å2
Refinement stepCycle: final / Resolution: 1.88→45.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 428 126 3694
Biso mean--44.87 32.8 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093434
X-RAY DIFFRACTIONf_angle_d1.2684626
X-RAY DIFFRACTIONf_chiral_restr0.051523
X-RAY DIFFRACTIONf_plane_restr0.007568
X-RAY DIFFRACTIONf_dihedral_angle_d24.3971258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8783-1.89960.33121310.33632573270495
1.8996-1.9220.35991320.33182611274399
1.922-1.94540.31981380.31162647278598
1.9454-1.97010.35771380.30872607274598
1.9701-1.9960.31631420.29482640278298
1.996-2.02330.27211360.27982596273297
2.0233-2.05220.3061390.26452629276899
2.0522-2.08290.311410.246226372778100
2.0829-2.11540.22141380.24162691282999
2.1154-2.15010.27461430.228126992842100
2.1501-2.18720.25061390.218926572796100
2.1872-2.22690.22421380.201526652803100
2.2269-2.26980.23061450.197926742819100
2.2698-2.31610.24521430.186826602803100
2.3161-2.36650.19371380.177526822820100
2.3665-2.42150.19581360.1732665280199
2.4215-2.48210.22541390.17412666280599
2.4821-2.54920.19671390.167426412780100
2.5492-2.62420.20791430.166426902833100
2.6242-2.70890.21091460.16462673281999
2.7089-2.80570.22921380.16872580271898
2.8057-2.9180.17821350.16122569270496
2.918-3.05080.20781390.172526762815100
3.0508-3.21160.20771420.171426812823100
3.2116-3.41270.19961420.184426392781100
3.4127-3.67610.24031400.191426742814100
3.6761-4.04580.21281440.19626902834100
4.0458-4.63080.19041430.196126582801100
4.6308-5.83240.23651390.23242600273997
5.8324-45.7130.26051380.212426662804100

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