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- PDB-3fid: LpxR from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 3fid
TitleLpxR from Salmonella typhimurium
ComponentsPutative outer membrane protein (LpxR)
KeywordsMEMBRANE PROTEIN / lipopolysaccharide-modifying outer membrane enzyme
Function / homology
Function and homology information


Outer membrane protein / Lipid A deacylase LpxR / Putative outer membrane protein superfamily / Outer membrane protein LpxR / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PENTAETHYLENE GLYCOL MONODECYL ETHER / Outer membrane protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, direct methodMULTI using P21212, P2 crystal / Resolution: 1.9 Å
AuthorsRutten, L. / Gros, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium
Authors: Rutten, L. / Mannie, J.-P.B.A. / Stead, C.M. / Raetz, C.R.H. / Reynolds, C.M. / Bonvin, A.M.J.J. / Tommassen, J.P. / Egmond, M.R. / Trent, M.S. / Gros, P.
History
DepositionDec 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.3Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative outer membrane protein (LpxR)
B: Putative outer membrane protein (LpxR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,82523
Polymers64,8402
Non-polymers3,98521
Water7,458414
1
A: Putative outer membrane protein (LpxR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,44512
Polymers32,4201
Non-polymers2,02511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Putative outer membrane protein (LpxR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,38011
Polymers32,4201
Non-polymers1,96010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.930, 127.650, 60.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative outer membrane protein (LpxR)


Mass: 32419.988 Da / Num. of mol.: 2 / Fragment: mature domain, UNP residues 24-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: strain LT2 / Gene: lpxr / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: Q8ZPT3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CXE / PENTAETHYLENE GLYCOL MONODECYL ETHER


Mass: 378.544 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H42O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 14% PEG 6000 (w/v), 10% glycerol (v/v), 50mM Tris-HCl, 5mM zinc chloride, pH 8.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2007 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→48.74 Å / Num. all: 66242 / Num. obs: 66190 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 14.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 15 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 3.6 / Num. unique all: 9516 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXCDphasing
SHELXEmodel building
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD, direct methodMULTI using P21212, P2 crystal
Resolution: 1.9→48.74 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.714 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22959 3357 5.1 %RANDOM
Rwork0.1907 ---
obs0.19266 62825 99.99 %-
all-66190 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.925 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.68 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 187 414 5189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224852
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9676516
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.265590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84323.947228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86615728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0981528
X-RAY DIFFRACTIONr_chiral_restr0.1080.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023666
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.22116
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23239
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2387
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1850.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0610.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.891.53011
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40724646
X-RAY DIFFRACTIONr_scbond_it2.37432124
X-RAY DIFFRACTIONr_scangle_it3.4324.51870
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% reflection
Rfree0.295 244 -
Rwork0.226 4577 -
obs--100 %

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