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- PDB-6h53: Crystal structure of Mycobacterium tuberculosis phosphatidylinosi... -

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Basic information

Entry
Database: PDB / ID: 6h53
TitleCrystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) in apo form
ComponentsCDP-diacylglycerol--inositol 3-phosphatidyltransferase
KeywordsTRANSFERASE / Phosphotransferase Glycerophospholipid metabolism Metal binding protein
Function / homology
Function and homology information


CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity / glycerophospholipid biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phospholipid biosynthetic process / plasma membrane => GO:0005886 / peptidoglycan-based cell wall / magnesium ion binding / plasma membrane
Similarity search - Function
Phosphatidylinositol phosphate synthase PgsA1 / CDP-alcohol phosphotransferase transmembrane (TM) domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID / Phosphatidylinositol phosphate synthase / Phosphatidylinositol phosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 23, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CDP-diacylglycerol--inositol 3-phosphatidyltransferase
B: CDP-diacylglycerol--inositol 3-phosphatidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,71111
Polymers46,5492
Non-polymers3,1629
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-80 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.726, 72.896, 102.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 17 through 114 or resid 116 through 209))
21(chain B and (resid 17 through 114 or resid 116 through 209))

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
11THRTHRASPASP(chain A and (resid 17 through 114 or resid 116 through 209))AA17 - 11417 - 114
12PROPROMETMET(chain A and (resid 17 through 114 or resid 116 through 209))AA116 - 209116 - 209
21THRTHRASPASP(chain B and (resid 17 through 114 or resid 116 through 209))BB17 - 11417 - 114
22PROPROMETMET(chain B and (resid 17 through 114 or resid 116 through 209))BB116 - 209116 - 209

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Components

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


Mass: 23274.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv / Gene: pgsA1, Rv2612c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rossetta2
References: UniProt: P9WPG6, UniProt: P9WPG7*PLUS, EC: 2.7.8.11
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UPL / UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID / UNKNOWN PHOSPHOLIPID FRAGMENT


Mass: 478.920 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H70

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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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 278 K / Method: lipidic cubic phase
Details: 33% PEG 400 (v/v), 0.1 M NaCl, 0.1 M MgSO4 , 0.1 M trisodium citrate dihydrate pH 6 and dCTP as an additive

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.4→45.196 Å / Num. obs: 12001 / % possible obs: 99.35 % / Redundancy: 6.6 % / Biso Wilson estimate: 52.36 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Rsym value: 0.011 / Net I/σ(I): 12.44
Reflection shellResolution: 2.4→3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.4783 / Mean I/σ(I) obs: 3.45 / Num. unique obs: 1166 / CC1/2: 0.948 / Rpim(I) all: 0.1976 / Rrim(I) all: 0.5182 / % possible all: 99.32

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.82 Å45.2 Å
Translation3.82 Å45.2 Å

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASER2.8.0phasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D91

5d91


Resolution: 2.9→41.91 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 600 5 %Random selection
Rwork0.2195 ---
obs0.2217 11999 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.42 Å2 / Biso mean: 50.342 Å2 / Biso min: 18.23 Å2
Refinement stepCycle: final / Resolution: 2.9→41.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 237 0 3092
Biso mean--55.74 --
Num. residues----381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093009
X-RAY DIFFRACTIONf_angle_d0.9874076
X-RAY DIFFRACTIONf_chiral_restr0.051477
X-RAY DIFFRACTIONf_plane_restr0.007497
X-RAY DIFFRACTIONf_dihedral_angle_d20.1421749
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2180X-RAY DIFFRACTION8.24TORSIONAL
12B2180X-RAY DIFFRACTION8.24TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9001-3.19180.25541480.20722799100
3.1918-3.65340.26971480.21522807100
3.6534-4.6020.26491490.19712843100
4.602-100.25631550.2465295099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0202-0.2630.0174.45831.38440.435-0.5680.65820.2212-0.6060.5568-0.3557-0.24721.59780.11920.2932-0.0756-0.03170.9146-0.10280.3646-1.56285.7805-7.5741
21.7957-1.2883-3.92981.93491.54592.0007-0.21141.27860.5167-0.49290.0807-0.29040.7638-0.55780.2150.3817-0.12920.12140.73670.0010.4316-4.584112.4013-7.2931
31.91210.10630.00221.83021.60354.6194-0.00060.13350.0622-0.1478-0.1083-0.0255-0.208-0.12630.09470.33930.04620.00140.3087-0.00140.281-18.47726.3409-4.5249
42.28251.94461.45512.41862.05041.7891-0.1110.83110.9477-0.3179-0.44240.1195-1.32160.39510.28420.72180.14930.06190.48290.25520.5326-25.060613.9347-17.5959
53.9059-0.9201-1.40043.6220.53042.937-0.0741-0.38680.49990.1476-0.42660.50870.46010.2680.26350.4653-0.10620.06210.40670.00750.315-12.557519.46795.518
64.60070.62021.45030.84140.29316.9552-0.34960.69140.6937-0.2252-0.44540.46390.2088-0.187-0.05560.39270.04930.010.27810.0050.3205-29.88714.3299-9.0964
71.4222-0.2667-0.46633.2391-0.14690.4982-0.03380.06520.0751-0.3808-0.22470.69270.5257-0.95910.03070.4509-0.1523-0.01180.85-0.17210.6853-44.2952-1.2935-7.0549
81.2963-0.534-0.73012.321-2.07623.19270.2190.4704-0.0325-0.6886-0.56480.63780.6513-0.56730.14660.6801-0.1009-0.15120.793-0.11490.6808-41.6608-6.2051-10.5704
92.1223-0.58222.33852.8662-1.18984.5780.2199-0.09530.0155-0.27-0.35370.36661.056-0.853-0.15440.333-0.05140.01370.3462-0.03660.2636-30.6146-0.112-2.5816
102.88160.1384-0.77952.0457-0.06931.39930.1606-0.0158-0.2759-0.1748-0.09150.11520.8157-0.490.05640.47690.0795-0.00380.2584-0.06610.3052-20.6277-3.9204-5.9377
116.1682-0.69831.00677.0938-4.27242.6312-0.160.6573-0.00980.22840.1792-0.06480.3658-0.07180.08150.7437-0.2252-0.08170.29730.04530.4173-30.4046-13.6234-0.9314
122.05370.63021.23061.7485-0.39581.17090.1636-0.0586-0.5570.0869-0.0483-0.04350.78620.13340.20780.54780.0286-0.09730.15380.04010.3823-19.9212-10.6811-7.2535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 53 )A17 - 53
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 76 )A54 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 141 )A77 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 152 )A142 - 152
5X-RAY DIFFRACTION5chain 'A' and (resid 153 through 173 )A153 - 173
6X-RAY DIFFRACTION6chain 'A' and (resid 174 through 209 )A174 - 209
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 53 )B16 - 53
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 82 )B54 - 82
9X-RAY DIFFRACTION9chain 'B' and (resid 83 through 111 )B83 - 111
10X-RAY DIFFRACTION10chain 'B' and (resid 112 through 152 )B112 - 152
11X-RAY DIFFRACTION11chain 'B' and (resid 153 through 166 )B153 - 166
12X-RAY DIFFRACTION12chain 'B' and (resid 167 through 209 )B167 - 209

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