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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 / homologyTgt2/MlaC / Tgt2/MlaC superfamily / Toluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Toluene tolerance protein
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.604 Å
AuthorsBhabha, G. / Ekiert, D.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM112982 United States
Damon Runyon Cancer Research FoundationDRG-2140-12 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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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
Polymers50,2632
Non-polymers2,7684
Water724
1
B: Toluene tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5153
Polymers25,1321
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
Polymers25,1321
Non-polymers1,3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP1211

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Components

#1: Protein Toluene tolerance protein


Mass: 25131.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 (E. 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 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 52.61 %

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.604→39.086 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 29.65
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 741 5.01 %RANDOM
Rwork0.2137 ---
obs0.2162 14801 92.28 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 2.604→39.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 176 4 3096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023153
X-RAY DIFFRACTIONf_angle_d0.544219
X-RAY DIFFRACTIONf_dihedral_angle_d12.8951267
X-RAY DIFFRACTIONf_chiral_restr0.025436
X-RAY DIFFRACTIONf_plane_restr0.003552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6036-2.80450.33061170.27012154X-RAY DIFFRACTION72
2.8045-3.08670.38691430.26372830X-RAY DIFFRACTION93
3.0867-3.53310.29871560.2332935X-RAY DIFFRACTION98
3.5331-4.45030.21861600.19093025X-RAY DIFFRACTION99
4.4503-39.09020.22081650.18843116X-RAY DIFFRACTION99
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)
10.0313-0.0117-0.07650.02070.06890.3397-0.05710.0172-0.04480.104-0.1327-0.28350.13430.0431-0.80120.1166-0.02620.06240.10390.08660.345425.4179-6.42067.4315
20.41410.16790.17780.26320.06120.30960.07060.0625-0.27140.037-0.0154-0.08970.08330.0380.32630.0762-0.07570.03080.1883-0.00880.233410.28234.634.8864
30.0759-0.0404-0.01220.11580.00640.1340.0349-0.00310.06790.0042-0.0005-0.06160.02640.01450.1340.32160.01270.1050.1602-0.12450.426828.8038-12.2302-2.7855
40.06580.0231-0.07730.0159-0.01020.12860.0117-0.0156-0.0296-0.012-0.0004-0.03140.0028-0.1023-0.03680.0979-0.02350.14680.2755-0.03390.464636.211810.42570.1042
50.011-0.0011-0.00120.0019-0.00340.00740.04210.03110.0546-0.0164-0.0068-0.0154-0.01830.00990.21140.208-0.02270.20190.2756-0.15110.49132.84-8.6258-10.099
60.1018-0.01-0.06630.0103-0.00790.0657-0.012-0.0777-0.03510.00670.0008-0.00530.00040.0114-0.11840.1302-0.02370.08060.2732-0.06130.531830.04887.14612.4887
70.3729-0.0465-0.06530.0099-0.0070.0619-0.01390.0915-0.0842-0.0164-0.0123-0.00370.0198-0.01110.00380.07470.00210.05940.10770.01350.278626.5474.684-1.3865
80.0496-0.03230.04720.2409-0.14970.1098-0.00540.08480.1639-0.0169-0.17620.0342-0.0302-0.0958-0.50250.12740.092-0.06260.3669-0.12360.34226.59376.6724-4.151
90.0563-0.0151-0.0510.07770.01720.0463-0.0490.0638-0.0108-0.08930.0140.0338-0.0126-0.04270.00160.2354-0.07740.01630.4709-0.05190.138511.8574-3.0738-9.0603
100.1207-0.15810.07090.2154-0.11450.1208-0.0196-0.0515-0.02650.1039-0.0165-0.1249-0.03060.09060.15470.5934-0.038-0.28590.20570.11470.467426.5-7.983430.763
110.22790.1581-0.22670.1638-0.26370.43520.05120.00460.05820.10390.07960.0364-0.1911-0.0460.40210.35990.0125-0.06850.1450.02860.125516.9404-0.818621.4928
120.2889-0.0693-0.04020.0522-0.07470.20420.0567-0.21170.00430.04810.0104-0.0197-0.11680.1350.27840.2092-0.0021-0.09940.1877-0.04490.16937.8264-25.168621.0719
130.36650.04690.11220.00750.00290.1846-0.0982-0.01070.19250.0888-0.01390.0144-0.40110.0698-0.04280.28140.0386-0.0240.1719-0.02440.09187.0586-12.470119.0947
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
150.0042-0.00910.00180.0269-0.01390.0149-0.0136-0.00890.01360.0549-0.0015-0.037-0.0477-0.0118-0.15460.64980.0545-0.26950.25320.07270.299925.0022-23.904837.4033
160.0140.00150.00210.0027-0.00360.00740.0458-0.0017-0.03460.024-0.0037-0.01190.02760.01580.22540.73070.1517-0.25770.336-0.12960.302216.5257-4.903644.1372
170.05080.04120.03520.1086-0.0070.04090.0329-0.10170.0380.0867-0.06690.0063-0.0851-0.01240.08730.4839-0.0254-0.26540.2108-0.05870.359221.2875-20.567132.0114
180.0033-0.02430.00710.1677-0.02830.0992-0.0161-0.0025-0.02710.2243-0.0670.0455-0.0378-0.0634-0.00360.299-0.1071-0.03130.174-0.03680.08626.6263-19.164731.0593
190.03290.0149-0.02830.0178-0.01140.02430.00010.0058-0.0084-0.01420.00730.0091-0.01010.0030.06670.153-0.0042-0.06180.2725-0.15920.3109-3.7222-19.756917.3408
200.00170.0050.00770.01320.0210.03360.0005-0.00240.0204-0.0161-0.0022-0.00940.0148-0.01-0.04220.27070.0180.09380.3018-0.07820.1611-0.4862-10.457431.7499
Refinement 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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