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- PDB-3gp6: Crystal structure of PagP in SDS/MPD -

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Basic information

Entry
Database: PDB / ID: 3gp6
TitleCrystal structure of PagP in SDS/MPD
ComponentsProtein pagP
KeywordsTRANSFERASE / PALMITOYLTRANSFERASE / BETA-BARREL / OUTER MEMBRANE ENZYME / PagP / SDS / MPD
Function / homology
Function and homology information


lipid IVA palmitoyltransferase / O-palmitoyltransferase activity / lipid A biosynthetic process / cell outer membrane
Similarity search - Function
Antimicrobial peptide resistance/lipid A acylation PagP / Antimicrobial peptide resistance and lipid A acylation protein PagP / Porin - #20 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Lipid A palmitoyltransferase PagP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCuesta-Seijo, J.A. / Prive, G.G.
CitationJournal: Structure / Year: 2010
Title: PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler.
Authors: Cuesta-Seijo, J.A. / Neale, C. / Khan, M.A. / Moktar, J. / Tran, C.D. / Bishop, R.E. / Pomes, R. / Prive, G.G.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Protein pagP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,61125
Polymers19,2401
Non-polymers3,37024
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.228, 113.228, 55.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein pagP / Protein crcA


Mass: 19240.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b0622, crcA, JW0617, ybeG / Plasmid: pET21(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37001

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Non-polymers , 6 types, 80 molecules

#2: Chemical
ChemComp-SDS / DODECYL SULFATE


Mass: 266.397 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26O4S / Comment: detergent*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1M MPD, 0.1M citrate pH 5.6, 1.7M lithium sulphate, 0.3M ammonium sulphate, SDS, Phase separation, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 40433 / Num. obs: 40433 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.068
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.36 / Num. unique all: 1633 / Rsym value: 0.531 / % possible all: 80.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
EPMRphasing
REFMAC5.2.0005refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1THQ

1thq


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.009 / SU ML: 0.05 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.062 / ESU R Free: 0.06 / Stereochemistry target values: Refmac 5
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The author states that the crystallization conditions included large amounts of lithium, but it cannot be confirmed that the ion is lithium ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The author states that the crystallization conditions included large amounts of lithium, but it cannot be confirmed that the ion is lithium based on electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.20817 1260 3.1 %RANDOM
Rwork0.17147 ---
all0.17259 39132 --
obs0.17259 39132 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.065 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å21.6 Å20 Å2
2--3.2 Å20 Å2
3----4.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 209 56 1523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211567
X-RAY DIFFRACTIONr_bond_other_d0.0020.021452
X-RAY DIFFRACTIONr_angle_refined_deg2.1192.0172146
X-RAY DIFFRACTIONr_angle_other_deg0.9633338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10822.89969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99115191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.014158
X-RAY DIFFRACTIONr_chiral_restr0.1370.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021592
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02332
X-RAY DIFFRACTIONr_nbd_refined0.2360.2246
X-RAY DIFFRACTIONr_nbd_other0.1930.21358
X-RAY DIFFRACTIONr_nbtor_refined0.1990.2682
X-RAY DIFFRACTIONr_nbtor_other0.0920.2911
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0420.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2170.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1050.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7931.5830
X-RAY DIFFRACTIONr_mcbond_other1.7261.5329
X-RAY DIFFRACTIONr_mcangle_it3.80621295
X-RAY DIFFRACTIONr_scbond_it4.1253882
X-RAY DIFFRACTIONr_scangle_it5.1344.5841
X-RAY DIFFRACTIONr_rigid_bond_restr2.61233632
X-RAY DIFFRACTIONr_sphericity_free15.265358
X-RAY DIFFRACTIONr_sphericity_bonded9.63832977
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 91 -
Rwork0.303 2364 -
obs--82.24 %

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