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- PDB-5uw2: Structure of E. coli MCE protein MlaD, periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 5uw2
TitleStructure of E. coli MCE protein MlaD, periplasmic domain
DescriptorProbable phospholipid ABC transporter-binding protein MlaD
KeywordsTRANSPORT PROTEIN / MCE protein / bacterial lipid transport
Specimen sourceEscherichia coli o157:h7 / bacteria / image: Escherichia coli
MethodX-ray diffraction (2.85 Å 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.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2017 / Release: Apr 12, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1Apr 19, 2017Structure modelDatabase references

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Assembly

Deposited unit
A: Probable phospholipid ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3119
Polyers53,9193
Non-polymers3926
Water0
#1
A: Probable phospholipid ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
hetero molecules

A: Probable phospholipid ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,62218
Polyers107,8376
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area (Å2)11210
ΔGint (kcal/M)-401
Surface area (Å2)33790
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)122.360, 63.820, 91.150
Angle α, β, γ (deg.)90.00, 130.01, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Polypeptide(L)Probable phospholipid ABC transporter-binding protein MlaD


Mass: 17972.891 Da / Num. of mol.: 3 / Fragment: UNP residues 32-183
Source: (gene. exp.) Escherichia coli o157:h7 / bacteria / image: Escherichia coli
References: UniProt: P64605
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Formula: Zn

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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: 2.53 / Density percent sol: 51.34
Crystal growTemp: 293 K / Method: VAPOR DIFFUSION, SITTING DROP
Details: 0.2 M zinc acetate, 0.1 M MES pH 6.0, and 15% ethanol

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 8.3.1 / Synchrotron site: ALS / Beamline: 8.3.1 / Wavelength: 1.116
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Collection date: Feb 20, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionD resolution high: 2.85 Å / D resolution low: 50 Å / Number obs: 12551 / CC half: 0.47 / NetI over sigmaI: 14.9 / Redundancy: 3.7 / Percent possible obs: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UW8
Overall SU ML: 0.37 / Cross valid method: FREE R-VALUE / Sigma F: 0 / Overall phase error: 34.63
Solvent computationSolvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1 Å
Least-squares processR factor R free: 0.2648 / R factor R work: 0.2394 / R factor obs: 0.2406 / Highest resolution: 2.85 Å / Lowest resolution: 33.599 Å / Number reflection R free: 589 / Number reflection obs: 11594 / Percent reflection R free: 5.08 / Percent reflection obs: 91.09
Refine hist #LASTHighest resolution: 2.85 Å / Lowest resolution: 33.599 Å
Number of atoms included #LASTProtein: 2557 / Nucleic acid: 0 / Ligand: 6 / Solvent: 0 / Total: 2563
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032596
X-RAY DIFFRACTIONf_angle_d0.7373526
X-RAY DIFFRACTIONf_dihedral_angle_d9.530950
X-RAY DIFFRACTIONf_chiral_restr0.028426
X-RAY DIFFRACTIONf_plane_restr0.003447
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
2.85000.37830.36203.1366126235679.00
3.13660.30910.28573.5901146276792.00
3.59010.29350.24224.5214158295298.00
4.52140.23230.216633.6015159293095.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
13.21030.1951-0.56653.8698-2.50002.47050.07330.0872-0.35000.45040.04210.0766-0.41680.51140.00071.04820.0227-0.25740.8943-0.10311.043117.981125.742719.6262
20.5456-1.4116-0.23293.50790.58473.29310.0637-0.02660.3590-0.00730.3160-0.7627-0.54390.76080.00060.8444-0.06320.01751.0014-0.15921.241225.749825.3126-5.6183
34.2259-1.77840.94342.67670.81632.7218-0.27930.21870.2141-0.42480.0666-0.0810-0.33310.27060.00021.1164-0.13220.11270.76700.03660.78188.103125.4868-25.0812
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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