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- PDB-4v35: The Structure of A-PGS from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4v35
TitleThe Structure of A-PGS from Pseudomonas aeruginosa
ComponentsALANYL-TRNA-DEPENDENT L-ALANYL- PHOPHATIDYLGLYCEROL SYNTHASE
KeywordsTRANSFERASE / TRNA-DEPENDENT AMINOACYLATION / BACTERIAL RESISTANCE PROTEINS / A-PGS / LIPID HOMEOSTASIS
Function / homology
Function and homology information


lysyltransferase / phosphatidylglycerol alanyltransferase activity / phosphatidylglycerol lysyltransferase activity / phospholipid homeostasis / lipid metabolic process / response to antibiotic / plasma membrane
Similarity search - Function
Lysylphosphatidylglycerol synthetase/glycosyltransferase AglD / Lysylphosphatidylglycerol synthase TM region / : / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETATE ION / Phosphatidylglycerol lysyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKrausze, J. / Hebecker, S. / Hasenkampf, T. / Heinz, D.W. / Moser, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structures of Two Bacterial Resistance Factors Mediating tRNA-Dependent Aminoacylation of Phosphatidylglycerol with Lysine or Alanine.
Authors: Hebecker, S. / Krausze, J. / Hasenkampf, T. / Schneider, J. / Groenewold, M. / Reichelt, J. / Jahn, D. / Heinz, D.W. / Moser, J.
History
DepositionOct 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALANYL-TRNA-DEPENDENT L-ALANYL- PHOPHATIDYLGLYCEROL SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,41717
Polymers38,4011
Non-polymers1,01616
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.180, 94.180, 166.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-2082-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ALANYL-TRNA-DEPENDENT L-ALANYL- PHOPHATIDYLGLYCEROL SYNTHASE


Mass: 38401.238 Da / Num. of mol.: 1 / Fragment: SOLUBLE DOMAIN, UNP RESIDUES 543-881 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET52B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I537, EC: 2.3.2.11

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Non-polymers , 7 types, 127 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 4.81 Å3/Da / Density % sol: 74.4 % / Description: NONE
Crystal growpH: 6.4
Details: 0.085 M NAAC PH 6.4, 1.6 M (NH4)2SO4, 20% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91842
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2013 / Details: SAGITALLY BENT SI111 CRYSTAL
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 33909 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.34
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 2.01 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.695 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 1694 5 %
Rwork0.1746 --
obs0.1758 33874 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 60 111 2701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082666
X-RAY DIFFRACTIONf_angle_d1.1093599
X-RAY DIFFRACTIONf_dihedral_angle_d14.507985
X-RAY DIFFRACTIONf_chiral_restr0.042375
X-RAY DIFFRACTIONf_plane_restr0.005479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36760.32871380.2682620X-RAY DIFFRACTION99
2.3676-2.44390.28541370.25182605X-RAY DIFFRACTION99
2.4439-2.5310.28521400.23862647X-RAY DIFFRACTION99
2.531-2.63210.25841380.2242638X-RAY DIFFRACTION100
2.6321-2.75160.24061380.22222624X-RAY DIFFRACTION99
2.7516-2.89630.26851400.20952669X-RAY DIFFRACTION100
2.8963-3.07710.22261400.20052655X-RAY DIFFRACTION100
3.0771-3.31370.22211420.19372693X-RAY DIFFRACTION100
3.3137-3.64520.19641410.15862692X-RAY DIFFRACTION100
3.6452-4.16840.1671440.14112720X-RAY DIFFRACTION100
4.1684-5.23530.14211450.12452761X-RAY DIFFRACTION100
5.2353-19.69550.15431510.15842856X-RAY DIFFRACTION98
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)
13.730.2321-0.57773.2192-0.47922.7246-0.044-0.2615-0.4162-0.05-0.0060.13330.4545-0.0280.04360.3256-0.0391-0.01670.32610.01670.213218.2122136.3181.441
24.1875-0.80281.3234.13430.64892.84960.06610.27840.058-0.4015-0.03260.27550.016-0.5083-0.04680.2374-0.0143-0.03920.59850.00780.3268200.1263153.5407171.6762
33.81-1.0336-0.70461.18530.08061.4455-0.04020.13690.3639-0.1736-0.01670.0351-0.0096-0.12710.06480.2724-0.0259-0.05220.3623-0.00040.2456217.7242154.2904172.2883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 546 THROUGH 662 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 663 THROUGH 766 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 767 THROUGH 872 )

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