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- PDB-3my2: Crystal structure of LptC -

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Basic information

Entry
Database: PDB / ID: 3my2
TitleCrystal structure of LptC
ComponentsLipopolysaccharide export system protein lptC
KeywordsTRANSPORT PROTEIN / LptC / lipopolysaccharide export pathway / Structural Genomics / Scottish Structural Proteomics Facility / SSPF
Function / homology
Function and homology information


lipopolysaccharide transmembrane transporter activity / transporter complex / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / outer membrane-bounded periplasmic space / membrane / identical protein binding / 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
Lipopolysaccharide export system protein LptC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsTran, A.X. / Dong, C. / Whitfield, C. / Scottish Structural Proteomics Facility (SSPF)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure and functional analysis of LptC, a conserved membrane protein involved in the lipopolysaccharide export pathway in Escherichia coli.
Authors: Tran, A.X. / Dong, C. / Whitfield, C.
History
DepositionMay 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide export system protein lptC


Theoretical massNumber of molelcules
Total (without water)20,2421
Polymers20,2421
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipopolysaccharide export system protein lptC

A: Lipopolysaccharide export system protein lptC


Theoretical massNumber of molelcules
Total (without water)40,4842
Polymers40,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.210, 94.210, 60.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lipopolysaccharide export system protein lptC


Mass: 20241.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. MG1655 / Gene: b3199, JW3166, lptC, yrbK / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P0ADV9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.04 M K2SO4, 16% PEG8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2008
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.2→37 Å / Num. all: 14286 / Num. obs: 14109 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.084 / Rsym value: 0.099 / Net I/σ(I): 15.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.709 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
REFMAC5.2.0019refinement
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.626 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22226 718 5 %RANDOM
Rwork0.19466 ---
obs0.19606 13542 99.53 %-
all-14286 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.628 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å2-0 Å20 Å2
2---1.83 Å20 Å2
3---3.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 0 71 1089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221037
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.9591407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04224.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93715177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.667156
X-RAY DIFFRACTIONr_chiral_restr0.1510.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02763
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.2350
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2702
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1591.5630
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21821024
X-RAY DIFFRACTIONr_scbond_it3.8493407
X-RAY DIFFRACTIONr_scangle_it6.0364.5381
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 70 -
Rwork0.331 970 -
obs--99.9 %
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)
14.6171-3.1588-0.97924.05610.98291.6022-0.0776-0.11990.1550.05680.0699-0.1966-0.1620.03820.00760.0317-0.0123-0.00530.03280.00280.05172.024127.76321.0721
23.0979-2.00140.08682.3028-0.09851.7435-0.0709-0.04040.03760.05830.07640.08440.0112-0.0354-0.00550.1241-0.0308-0.00420.15180.00340.1328-0.426527.45130.2134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 184
2X-RAY DIFFRACTION2A192 - 262

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