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- PDB-5uwa: Structure of E. coli phospholipid binding protein MlaC -

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Basic information

Entry
Database: PDB / ID: 5uwa
TitleStructure of E. coli phospholipid binding protein MlaC
DescriptorProbable phospholipid-binding protein MlaC
KeywordsTRANSPORT PROTEIN / phospholipid-binding protein / bacterial lipid transport
Specimen sourceEscherichia coli (strain k12) / bacteria /
MethodX-ray diffraction (1.501 A resolution / Molecular replacement)
AuthorsBhabha, G. / Ekiert, D.C.
CitationCell, 2017, 169, 273-285.e17

Cell, 2017, 169, 273-285.e17 StrPapers
Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Ekiert, D.C. / Bhabha, G. / Isom, G.L. / Greenan, G. / Ovchinnikov, S. / Henderson, I.R. / Cox, J.S. / Vale, R.D.

DateDeposition: Feb 20, 2017 / Release: Apr 12, 2017 / Last modification: Apr 19, 2017

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Assembly

Deposited unit
A: Probable phospholipid-binding protein MlaC
B: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2494
Polyers47,0252
Non-polymers1,2242
Water5,206289
#1
A: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1252
Polyers23,5131
Non-polymers6121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#2
B: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1252
Polyers23,5131
Non-polymers6121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
gamma
alpha
beta
Length a, b, c (A): 33.630, 115.890, 133.220 / Angle α, β, γ (deg.): 90.00, 90.00, 90.00

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Components

#1: Polypeptide(L)Probable phospholipid-binding protein MlaC


Mass: 23512.613 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli (strain k12) / bacteria /
References: UniProt: P0ADV7

Cellular component

Molecular function

Biological process

#2: ChemicalChemComp-8ND / (2S)-3-(2-aminoethoxy)propane-1,2-diyl dihexadecanoate


Mass: 611.979 Da / Num. of mol.: 2 / Formula: C37H73NO5
#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.76 / Density percent sol: 55.44
Crystal growTemp: 295 K / Method: VAPOR DIFFUSION, SITTING DROP
Details: 0.1 M citric acid pH 3.5 and 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 8.3.1 / Synchrotron site: ALS / Beamline: 8.3.1 / Wavelength: 1.116
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Collection date: May 21, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 / Relative weight: 1
ReflectionD resolution high: 1.5 / D resolution low: 50 / Number obs: 83295 / CC half: 0.57 / NetI over sigmaI: 22.2 / Redundancy: 7.2 / Percent possible obs: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ComputingStructure refinement: PHENIX (phenix.refine: 1.9_1692)
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: based on homology model with 2QGU as a template
Overall SU ML: 0.16 / Cross valid method: FREE R-VALUE / Sigma F: 0 / Overall phase error: 17.02
Solvent computationSolvent shrinkage radii: 0.9 / Solvent vdw probe radii: 1.2
Least-squares processR factor R free: 0.1675 / R factor R work: 0.138 / R factor obs: 0.1387 / Highest resolution: 1.501 / Lowest resolution: 43.718 / Number reflection R free: 1894 / Number reflection obs: 79050 / Percent reflection R free: 2.4 / Percent reflection obs: 93.56
Refine hist #LASTHighest resolution: 1.501 / Lowest resolution: 43.718
Number of atoms included #LASTProtein: 2978 / Nucleic acid: 0 / Ligand: 80 / Solvent: 289 / Total: 3347
Refine LS restraints
Refine idTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093310
X-RAY DIFFRACTIONf_angle_d1.2024497
X-RAY DIFFRACTIONf_dihedral_angle_d14.1561316
X-RAY DIFFRACTIONf_chiral_restr0.046478
X-RAY DIFFRACTIONf_plane_restr0.006590
Refine LS shell

Refine id: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.50120.32450.25931.5387119466080.00
1.53870.26420.20641.5803114482584.00
1.58030.23920.18101.6268123505087.00
1.62680.23140.16141.6793130522289.00
1.67930.18990.13601.7394130532092.00
1.73940.19660.12391.8090131542793.00
1.80900.17400.11401.8913134557195.00
1.89130.17060.10761.9910140566397.00
1.99100.16120.10682.1158141574698.00
2.11580.15690.10872.2791142577398.00
2.27910.15330.12122.5085144581899.00
2.50850.16180.13852.8714146592099.00
2.87140.13810.14293.6174147594899.00
3.61740.17030.150443.7366153621399.00

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