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- PDB-4v34: The Structure of A-PGS from Pseudomonas aeruginosa (SeMet derivative) -

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Basic information

Entry
Database: PDB / ID: 4v34
TitleThe Structure of A-PGS from Pseudomonas aeruginosa (SeMet derivative)
ComponentsALANYL-TRNA-DEPENDENT L-ALANYL- PHOPHATIDYLGLYCEROL SYNTHASE
KeywordsTRANSFERASE / SAD / 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
Phosphatidylglycerol lysyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 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 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,1226
Polymers38,8231
Non-polymers2985
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.690, 93.690, 166.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 38823.289 Da / Num. of mol.: 1 / Fragment: SOLUBLE DOMAIN, UNP RESIDUES 543-881 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SELENO-METHIONINE DERIVATIVE / 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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 4.74 Å3/Da / Density % sol: 74.05 % / Description: NONE
Crystal growpH: 5.7
Details: 0.085M MES PH 5.7; 1.53M (NH4)2SO4; 15%(V/V) GLYCEROL; 0.0075M COCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97974
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2012 / Details: SAGITALLY BENT SI111 CRYSTAL
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97974 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 25682 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Biso Wilson estimate: 55.14 Å2 / Rmerge(I) obs: 0.31 / Net I/σ(I): 10.1
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.1→47.678 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 1302 5.1 %
Rwork0.1816 --
obs0.1832 25677 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.6 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 13 0 2581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022659
X-RAY DIFFRACTIONf_angle_d0.6373601
X-RAY DIFFRACTIONf_dihedral_angle_d12.252995
X-RAY DIFFRACTIONf_chiral_restr0.025378
X-RAY DIFFRACTIONf_plane_restr0.003477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1003-3.22440.31261450.27132785X-RAY DIFFRACTION100
3.2244-3.37120.27251380.24092671X-RAY DIFFRACTION100
3.3712-3.54880.28711410.21092692X-RAY DIFFRACTION100
3.5488-3.77110.20031460.18352709X-RAY DIFFRACTION100
3.7711-4.06210.19761440.16232707X-RAY DIFFRACTION100
4.0621-4.47060.18941490.13962723X-RAY DIFFRACTION100
4.4706-5.11690.14911470.14132684X-RAY DIFFRACTION100
5.1169-6.44420.22141420.18352702X-RAY DIFFRACTION100
6.4442-47.6840.20721500.19012702X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 211.404 Å / Origin y: 146.7349 Å / Origin z: 174.7512 Å
111213212223313233
T0.0827 Å2-0.0128 Å2-0.0344 Å2-0.2383 Å2-0.0015 Å2--0.1584 Å2
L0.432 °20.0149 °20.0334 °2-0.2205 °20.0744 °2--0.5091 °2
S-0.078 Å °0.0011 Å °0.015 Å °-0.0502 Å °-0.0032 Å °0.0171 Å °0.096 Å °-0.1608 Å °-0.0139 Å °
Refinement TLS groupSelection details: ALL

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