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- PDB-2erv: Crystal structure of the outer membrane enzyme PagL -

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Basic information

Entry
Database: PDB / ID: 2erv
TitleCrystal structure of the outer membrane enzyme PagL
Componentshypothetical protein Paer03002360Hypothesis
KeywordsMEMBRANE PROTEIN / Beta barrel / outer membrane / enzyme / hydrolase / lipopolysaccharide
Function / homology
Function and homology information


lipid A metabolic process / acyloxyacyl hydrolase / acyloxyacyl hydrolase activity / lipopolysaccharide metabolic process / cell outer membrane / membrane => GO:0016020 / protein homodimerization activity
Similarity search - Function
Lipid A 3-O-deacylase-related / Lipid A 3-O-deacylase (PagL) / Porin - #20 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PENTAETHYLENE GLYCOL MONODECYL ETHER / Lipid A deacylase PagL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRutten, L. / Geurtsen, J. / Lambert, W. / Smolenaers, J.J. / Bonvin, A.M. / van der Ley, P. / Egmond, M.R. / Gros, P. / Tommassen, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa.
Authors: Rutten, L. / Geurtsen, J. / Lambert, W. / Smolenaers, J.J. / Bonvin, A.M. / de Haan, A. / van der Ley, P. / Egmond, M.R. / Gros, P. / Tommassen, J.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Remark 600 HETEROGEN ONLY PARTS OF PENTAETHYLENE GLYCOL MONODECYL ETHER MOLECULES COULD BE MODELED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein Paer03002360
B: hypothetical protein Paer03002360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,79415
Polymers32,2112
Non-polymers4,58313
Water2,180121
1
A: hypothetical protein Paer03002360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6606
Polymers16,1061
Non-polymers1,5545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein Paer03002360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1349
Polymers16,1061
Non-polymers3,0288
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.264, 48.993, 105.026
Angle α, β, γ (deg.)90.00, 115.46, 90.00
Int Tables number5
Space group name H-MC121
DetailsPagL is a monomer

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Components

#1: Protein hypothetical protein Paer03002360 / Hypothesis


Mass: 16105.675 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA4661 / Plasmid: pPagL(Pa)(-) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q9HVD1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CXE / PENTAETHYLENE GLYCOL MONODECYL ETHER


Mass: 378.544 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H42O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3000, glycerol, calcium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 28914 / Num. obs: 26464 / % possible obs: 90.3 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3.7 / Redundancy: 3.1 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Χ2: 1.026 / Net I/σ(I): 20.9
Reflection shellResolution: 2→2.05 Å / % possible obs: 52.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3 / Num. measured obs: 1027 / Num. unique all: 1027 / Rsym value: 0.38 / Χ2: 1.124 / % possible all: 52.2

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Phasing

Phasing dmFOM : 0.55 / FOM acentric: 0.55 / FOM centric: 0.55 / Reflection: 21114 / Reflection acentric: 19959 / Reflection centric: 1155
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-28.4550.860.870.78936802134
3.9-6.30.910.920.8228572630227
3.1-3.90.840.850.6835603349211
2.8-3.10.630.630.5235533384169
2.4-2.80.370.370.3363276060267
2.2-2.40.190.190.1838813734147

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVE2.06phasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alanine model of NspA (1P4T) lacking the loops and turns.

1p4t


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.876 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1336 5.1 %RANDOM
Rwork0.198 ---
all0.2 28914 --
obs0.2 26283 90.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.36 Å2
2--0.19 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 136 121 2518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212416
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.9393225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89223.592103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12115311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.876159
X-RAY DIFFRACTIONr_chiral_restr0.1390.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021821
X-RAY DIFFRACTIONr_nbd_refined0.2060.2984
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21590
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2179
X-RAY DIFFRACTIONr_metal_ion_refined0.1090.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.28
X-RAY DIFFRACTIONr_mcbond_it1.1361.51460
X-RAY DIFFRACTIONr_mcangle_it1.80322254
X-RAY DIFFRACTIONr_scbond_it2.86931130
X-RAY DIFFRACTIONr_scangle_it3.8654.5971
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 52 -
Rwork0.186 1119 -
all-1171 -
obs--55.47 %
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)
10.7317-0.2081-0.32090.17070.33920.80170.07690.01150.167-0.02090.0262-0.03550.1035-0.0686-0.1031-0.0088-0.02520.0125-0.0239-0.0075-0.011616.153423.419924.6423
20.661-0.37650.25320.3097-0.24030.8320.07510.0236-0.0688-0.0132-0.04480.0048-0.09450.0705-0.0303-0.0038-0.0223-0.0066-0.00970.0001-0.038633.959942.931123.9356
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 150 / Label seq-ID: 1 - 150

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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