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- PDB-1thq: Crystal Structure of Outer Membrane Enzyme PagP -

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Basic information

Entry
Database: PDB / ID: 1thq
TitleCrystal Structure of Outer Membrane Enzyme PagP
ComponentsCrcA protein
KeywordsTRANSFERASE / palmitoyltransferase / beta-barrel / outer membrane enzyme / pagp
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
ACETATE ION / Lipid A palmitoyltransferase PagP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsAhn, V.E. / Lo, E.I. / Engel, C.K. / Chen, L. / Hwang, P.M. / Kay, L.E. / Bishop, R.E. / Prive, G.G.
CitationJournal: Embo J. / Year: 2004
Title: A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin.
Authors: Ahn, V.E. / Lo, E.I. / Engel, C.K. / Chen, L. / Hwang, P.M. / Kay, L.E. / Bishop, R.E. / Prive, G.G.
History
DepositionJun 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: CrcA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,87713
Polymers20,1981
Non-polymers1,67912
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.670, 50.670, 158.480
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 CrcA protein


Mass: 20198.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CRCA, B0622 / Plasmid: PET-21(A) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37001
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: MPD, sodium acetate, ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9505 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9505 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 17041 / Num. obs: 17041 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 13 %
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 11 % / Rmerge(I) obs: 0.337 / Num. unique all: 1648 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→18.29 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.883 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25546 828 4.9 %RANDOM
Rwork0.21648 ---
obs0.21842 16230 100 %-
all-16230 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 102 38 1364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9431849
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021063
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2511
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8441.5744
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46321175
X-RAY DIFFRACTIONr_scbond_it2.1283624
X-RAY DIFFRACTIONr_scangle_it3.3014.5674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.253 57
Rwork0.226 1187
Refinement TLS params.Method: refined / Origin x: 14.1345 Å / Origin y: 46.6247 Å / Origin z: 6.7657 Å
111213212223313233
T0.0327 Å20.0545 Å20.0135 Å2-0.0951 Å20.0403 Å2--0.0789 Å2
L2.5926 °20.1547 °2-0.3582 °2-2.3294 °20.6801 °2--4.2459 °2
S0.0919 Å °0.3416 Å °0.0464 Å °-0.1712 Å °0.0828 Å °-0.1663 Å °-0.3557 Å °-0.1217 Å °-0.1747 Å °

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