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- PDB-5uwb: Re-refined 4FCZ: lipid-bound crystal structure of toluene-toleran... -

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Basic information

Entry
Database: PDB / ID: 5uwb
TitleRe-refined 4FCZ: lipid-bound crystal structure of toluene-tolerance protein from Pseudomonas putida
ComponentsToluene tolerance protein
KeywordsTRANSPORT PROTEIN / Lipid-binding / periplasmic / MlaC / transport
Function / homologyToluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / Toluene tolerance protein
Function and homology information
Specimen sourcePseudomonas putida / / bacteria
MethodX-RAY DIFFRACTION / SAD / 2.604 Å resolution
AuthorsBhabha, G. / Ekiert, D.C.
Citation
Journal: Cell / Year: 2017
Title: Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Authors: Damian C Ekiert / Gira Bhabha / Georgia L Isom / Garrett Greenan / Sergey Ovchinnikov / Ian R Henderson / Jeffery S Cox / Ronald D Vale
Abstract: How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) ...How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) protein family form hexameric assemblies with a central channel capable of mediating lipid transport. The E. coli MCE protein, MlaD, forms a ring associated with an ABC transporter complex in the inner membrane. A soluble lipid-binding protein, MlaC, ferries lipids between MlaD and an outer membrane protein complex. In contrast, EM structures of two other E. coli MCE proteins show that YebT forms an elongated tube consisting of seven stacked MCE rings, and PqiB adopts a syringe-like architecture. Both YebT and PqiB create channels of sufficient length to span the periplasmic space. This work reveals diverse architectures of highly conserved protein-based channels implicated in the transport of lipids between the membranes of bacteria and some eukaryotic organelles.
Copyright: 2017 Elsevier Inc. All rights reserved.
#original_data_1: Journal: To be Published
Title: Northeast Structural Genomics Consortium Target PpR99
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2017 / Release: Apr 19, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 19, 2017Structure modelrepositoryInitial release
1.1Jun 14, 2017Structure modelStructure summarystruct_struct.title
1.2Sep 13, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
Remark 0THIS ENTRY 5UWB REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R4FCZSF DETERMINED ...THIS ENTRY 5UWB REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R4FCZSF DETERMINED BY AUTHORS OF THE PDB ENTRY 4FCZ: AUTHORS A.KUZIN, M.SU, J.SEETHARAMAN, S.SAHDEV, R.XIAO, C.CICCOSANTI, H.WANG, J.K.EVERETT, T.B.ACTON, G.T.MONTELIONE, L.TONG, J.F.HUNT, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)
Remark 200AUTHOR USED THE SF DATA FROM ENTRY 4FCZ.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Toluene tolerance protein
A: Toluene tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0316
Polyers50,2632
Non-polymers2,7684
Water724
1
B: Toluene tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5153
Polyers25,1321
Non-polymers1,3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Toluene tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5153
Polyers25,1321
Non-polymers1,3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)79.868, 40.883, 82.399
Angle α, β, γ (deg.)90.00, 106.49, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide Toluene tolerance protein


Mass: 25131.518 Da / Num. of mol.: 2
Source: (gene. exp.) Pseudomonas putida (strain atcc 47054 / dsm 6125 / ncimb 11950 / kt2440) / / bacteria
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: ttg2D, PP_0961 / Production host: Escherichia coli / References: UniProt:Q88P91
#2: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 4 / Formula: C37H74NO8P / Comment: phospholipid *YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Formula: H2O / Water

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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: 2.6 / Density percent sol: 52.61

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefineMethod to determine structure: SAD / Overall SU ML: 0.39 / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / Sigma F: 0.12 / Overall phase error: 29.65
Solvent computationSolvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1 Å
Least-squares processR factor R free: 0.2625 / R factor R work: 0.2137 / R factor obs: 0.2162 / Highest resolution: 2.604 Å / Lowest resolution: 39.086 Å / Number reflection R free: 741 / Number reflection obs: 14801 / Percent reflection R free: 5.01 / Percent reflection obs: 92.28
Refine hist #LASTHighest resolution: 2.604 Å / Lowest resolution: 39.086 Å
Number of atoms included #LASTProtein: 2916 / Nucleic acid: 0 / Ligand: 176 / Solvent: 4 / Total: 3096
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023153
X-RAY DIFFRACTIONf_angle_d0.5404219
X-RAY DIFFRACTIONf_dihedral_angle_d12.8951267
X-RAY DIFFRACTIONf_chiral_restr0.025436
X-RAY DIFFRACTIONf_plane_restr0.003552
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
2.60360.33060.27012.8045117215472.00
2.80450.38690.26373.0867143283093.00
3.08670.29870.23303.5331156293598.00
3.53310.21860.19094.4503160302599.00
4.45030.22080.188439.0902165311699.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.0313-0.0117-0.07650.02070.06890.3397-0.05710.0172-0.04480.1040-0.1327-0.28350.13430.0431-0.80120.1166-0.02620.06240.10390.08660.345425.4179-6.42067.4315
20.41410.16790.17780.26320.06120.30960.07060.0625-0.27140.0370-0.0154-0.08970.08330.03800.32630.0762-0.07570.03080.1883-0.00880.233410.28234.63004.8864
30.0759-0.0404-0.01220.11580.00640.13400.0349-0.00310.06790.0042-0.0005-0.06160.02640.01450.13400.32160.01270.10500.1602-0.12450.426828.8038-12.2302-2.7855
40.06580.0231-0.07730.0159-0.01020.12860.0117-0.0156-0.0296-0.0120-0.0004-0.03140.0028-0.1023-0.03680.0979-0.02350.14680.2755-0.03390.464636.211810.42570.1042
50.0110-0.0011-0.00120.0019-0.00340.00740.04210.03110.0546-0.0164-0.0068-0.0154-0.01830.00990.21140.2080-0.02270.20190.2756-0.15110.491032.8400-8.6258-10.0990
60.1018-0.0100-0.06630.0103-0.00790.0657-0.0120-0.0777-0.03510.00670.0008-0.00530.00040.0114-0.11840.1302-0.02370.08060.2732-0.06130.531830.04887.14612.4887
70.3729-0.0465-0.06530.0099-0.00700.0619-0.01390.0915-0.0842-0.0164-0.0123-0.00370.0198-0.01110.00380.07470.00210.05940.10770.01350.278626.54704.6840-1.3865
80.0496-0.03230.04720.2409-0.14970.1098-0.00540.08480.1639-0.0169-0.17620.0342-0.0302-0.0958-0.50250.12740.0920-0.06260.3669-0.12360.34226.59376.6724-4.1510
90.0563-0.0151-0.05100.07770.01720.0463-0.04900.0638-0.0108-0.08930.01400.0338-0.0126-0.04270.00160.2354-0.07740.01630.4709-0.05190.138511.8574-3.0738-9.0603
100.1207-0.15810.07090.2154-0.11450.1208-0.0196-0.0515-0.02650.1039-0.0165-0.1249-0.03060.09060.15470.5934-0.0380-0.28590.20570.11470.467426.5000-7.983430.7630
110.22790.1581-0.22670.1638-0.26370.43520.05120.00460.05820.10390.07960.0364-0.1911-0.04600.40210.35990.0125-0.06850.14500.02860.125516.9404-0.818621.4928
120.2889-0.0693-0.04020.0522-0.07470.20420.0567-0.21170.00430.04810.0104-0.0197-0.11680.13500.27840.2092-0.0021-0.09940.1877-0.04490.16937.8264-25.168621.0719
130.36650.04690.11220.00750.00290.1846-0.0982-0.01070.19250.0888-0.01390.0144-0.40110.0698-0.04280.28140.0386-0.02400.1719-0.02440.09187.0586-12.470119.0947
140.1771-0.01470.01030.25980.11370.05170.1072-0.0325-0.00510.04620.0428-0.07140.15580.11120.15890.57480.06580.02570.2196-0.03580.148917.3563-1.258335.7376
150.0042-0.00910.00180.0269-0.01390.0149-0.0136-0.00890.01360.0549-0.0015-0.0370-0.0477-0.0118-0.15460.64980.0545-0.26950.25320.07270.299925.0022-23.904837.4033
160.01400.00150.00210.0027-0.00360.00740.0458-0.0017-0.03460.0240-0.0037-0.01190.02760.01580.22540.73070.1517-0.25770.3360-0.12960.302216.5257-4.903644.1372
170.05080.04120.03520.1086-0.00700.04090.0329-0.10170.03800.0867-0.06690.0063-0.0851-0.01240.08730.4839-0.0254-0.26540.2108-0.05870.359221.2875-20.567132.0114
180.0033-0.02430.00710.1677-0.02830.0992-0.0161-0.0025-0.02710.2243-0.06700.0455-0.0378-0.0634-0.00360.2990-0.1071-0.03130.1740-0.03680.08626.6263-19.164731.0593
190.03290.0149-0.02830.0178-0.01140.02430.00010.0058-0.0084-0.01420.00730.0091-0.01010.00300.06670.1530-0.0042-0.06180.2725-0.15920.3109-3.7222-19.756917.3408
200.00170.00500.00770.01320.02100.03360.0005-0.00240.0204-0.0161-0.0022-0.00940.0148-0.0100-0.04220.27070.01800.09380.3018-0.07820.1611-0.4862-10.457431.7499
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 23 through 75 )
2X-RAY DIFFRACTION2chain 'B' and (resid 76 through 104 )
3X-RAY DIFFRACTION3chain 'B' and (resid 105 through 120 )
4X-RAY DIFFRACTION4chain 'B' and (resid 121 through 132 )
5X-RAY DIFFRACTION5chain 'B' and (resid 133 through 145 )
6X-RAY DIFFRACTION6chain 'B' and (resid 146 through 155 )
7X-RAY DIFFRACTION7chain 'B' and (resid 156 through 168 )
8X-RAY DIFFRACTION8chain 'B' and (resid 169 through 194 )
9X-RAY DIFFRACTION9chain 'B' and (resid 195 through 209 )
10X-RAY DIFFRACTION10chain 'A' and (resid 23 through 43 )
11X-RAY DIFFRACTION11chain 'A' and (resid 44 through 66 )
12X-RAY DIFFRACTION12chain 'A' and (resid 67 through 87 )
13X-RAY DIFFRACTION13chain 'A' and (resid 88 through 104 )
14X-RAY DIFFRACTION14chain 'A' and (resid 105 through 120 )
15X-RAY DIFFRACTION15chain 'A' and (resid 121 through 132 )
16X-RAY DIFFRACTION16chain 'A' and (resid 133 through 145 )
17X-RAY DIFFRACTION17chain 'A' and (resid 146 through 155 )
18X-RAY DIFFRACTION18chain 'A' and (resid 156 through 184 )
19X-RAY DIFFRACTION19chain 'A' and (resid 185 through 194 )
20X-RAY DIFFRACTION20chain 'A' and (resid 195 through 209 )

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