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

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Entry
Database: PDB / ID: 5uwb
TitleRe-refined 4FCZ: lipid-bound crystal structure of toluene-tolerance protein from Pseudomonas putida
DescriptorToluene tolerance protein
KeywordsTRANSPORT PROTEIN / Lipid-binding / periplasmic / MlaC / transport
Specimen sourcePseudomonas putida (strain atcc 47054 / dsm 6125 / ncimb 11950 / kt2440) / bacteria / MlaC
MethodX-ray diffraction (2.604 Å resolution / SAD)
AuthorsBhabha, G. / Ekiert, D.C.
CitationCell, 2017, 169, 273-285.e17

primary. Cell, 2017, 169, 273-285.e17 Yorodumi Papers
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.

original_data_1. To be Published Search PubMed
Northeast Structural Genomics Consortium Target PpR99
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 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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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: Polypeptide(L)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
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
#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.6 / 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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