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- PDB-4b54: The Structure of the inactive mutant G153R of LptC from E. coli -

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Basic information

Entry
Database: PDB / ID: 4b54
TitleThe Structure of the inactive mutant G153R of LptC from E. coli
ComponentsLIPOPOLYSACCHARIDE EXPORT SYSTEM PROTEIN LPTC
KeywordsTRANSPORT PROTEIN / INACTIVE MUTANT
Function / homology
Function and homology information


lipopolysaccharide transmembrane transporter activity / glycolipid transfer activity / transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane
Similarity search - Function
Lipopolysaccharide (LPS) transport protein A like domain / Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / : / Lipopolysaccharide-assembly, LptC-related / lipopolysaccharide transport protein A fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / Lipopolysaccharide export system protein LptC
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVilla, R. / Martorana, A.M. / Sperandeo, P. / Kahne, D. / Okuda, S. / Gourlay, L.J. / Nardini, M. / Bolognesi, M. / Polissi, A.
CitationJournal: J.Bacteriol. / Year: 2013
Title: The Escherichia Coli Lpt Transenvelope Protein Complex for Lipopolysaccharide Export is Assembled Via Conserved Structurally Homologous Domains.
Authors: Villa, R. / Martorana, A.M. / Okuda, S. / Gourlay, L.J. / Nardini, M. / Sperandeo, P. / Deho, G. / Bolognesi, M. / Kahne, D. / Polissi, A.
History
DepositionAug 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPOPOLYSACCHARIDE EXPORT SYSTEM PROTEIN LPTC
B: LIPOPOLYSACCHARIDE EXPORT SYSTEM PROTEIN LPTC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5223
Polymers40,4632
Non-polymers591
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-6.2 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.940, 98.280, 123.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LIPOPOLYSACCHARIDE EXPORT SYSTEM PROTEIN LPTC / LIPOSACCHARIDE TRANSPORT PROTEIN C


Mass: 20231.459 Da / Num. of mol.: 2 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 21-191 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: I2Z3T4, UniProt: P0ADV9*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.3 Å3/Da / Density % sol: 52.5 % / Description: NONE
Crystal growpH: 5.5
Details: STURA FOOTPRINT SCREEN NUMBER 1 CONDITION 18.2 (MOLECULAR DIMENSIONS) 18% PEG5K MME, 0.1M SODIUM ACETATE PH 5.5 PLUS 30% GLYCEROL FOR CRYOCOOLING

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 12846 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 3.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MY2

3my2


Resolution: 2.8→40 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.917 / SU B: 32.573 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26551 621 4.9 %RANDOM
Rwork0.24035 ---
obs0.24155 12169 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.04 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20 Å2
2---1.61 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 4 11 2048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222072
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9141.9522812
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8165248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49623.93999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1981516
X-RAY DIFFRACTIONr_chiral_restr0.0640.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021538
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.56331251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01442040
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4923821
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8124772
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.523 46 -
Rwork0.427 885 -
obs--98.94 %
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)
12.302-1.04960.93844.5796-0.7684.4424-0.03790.1094-0.0366-0.2527-0.006-0.14210.142-0.01190.04390.0352-0.03830.0170.0895-0.00970.041411.4775-22.8043-13.4486
21.8921-3.12741.84527.6808-4.6673.13220.0104-0.2335-0.1572-0.07110.24260.16980.1897-0.3099-0.2530.1908-0.0073-0.05480.23360.08010.1721-7.24425.08-27.2834
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 182
2X-RAY DIFFRACTION2B59 - 183

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