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- PDB-8g52: Crystal structure of a bacterial TPAT family transporter -

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Basic information

Entry
Database: PDB / ID: 8g52
TitleCrystal structure of a bacterial TPAT family transporter
ComponentsTPR_REGION domain-containing protein
KeywordsLIPID BINDING PROTEIN / TPAT family / lipid / transport
Function / homology
Function and homology information


TRAP transporter T-component / TRAP transporter T-component / TRAP transporter T-component superfamily / TRAP transporter T-component / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
PALMITIC ACID / Lipoprotein
Similarity search - Component
Biological speciesEnhygromyxa salina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsDassama, L.M.K. / Zhai, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2023
Title: Structures and Mechanisms of a Novel Bacterial Transport System for Fatty Acids.
Authors: Zhai, L. / Chou, J.C. / Oo, H. / Dassama, L.M.K.
History
DepositionFeb 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TPR_REGION domain-containing protein
B: TPR_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5404
Polymers72,0272
Non-polymers5132
Water3,711206
1
A: TPR_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2702
Polymers36,0131
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TPR_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2702
Polymers36,0131
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.695, 85.409, 73.686
Angle α, β, γ (deg.)90.000, 90.140, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z

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Components

#1: Protein TPR_REGION domain-containing protein


Mass: 36013.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enhygromyxa salina (bacteria) / Gene: DB30_07757 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0C2DGE5
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.87 Å3/Da / Density % sol: 34.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30 % (w/v) PEG 3000, 0.1 M Tris: HCl, pH 7,0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.88→38.19 Å / Num. obs: 42298 / % possible obs: 98.11 % / Redundancy: 4.2 % / Biso Wilson estimate: 32.65 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.43
Reflection shellResolution: 1.88→1.947 Å / Num. unique obs: 4283 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→38.19 Å / SU ML: 0.2197 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 2115 5 %
Rwork0.1827 40183 -
obs0.1846 42298 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.68 Å2
Refinement stepCycle: LAST / Resolution: 1.88→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 36 206 4548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734444
X-RAY DIFFRACTIONf_angle_d0.7926010
X-RAY DIFFRACTIONf_chiral_restr0.0394628
X-RAY DIFFRACTIONf_plane_restr0.0091780
X-RAY DIFFRACTIONf_dihedral_angle_d7.4605634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.920.34181370.30652601X-RAY DIFFRACTION97.23
1.92-1.970.28491420.26342686X-RAY DIFFRACTION98.43
1.97-2.020.30291420.25332693X-RAY DIFFRACTION97.83
2.02-2.080.30671380.24482637X-RAY DIFFRACTION96.42
2.08-2.150.28181410.2142657X-RAY DIFFRACTION98.73
2.15-2.230.26181420.20762700X-RAY DIFFRACTION99.02
2.23-2.320.2491410.22684X-RAY DIFFRACTION98.26
2.32-2.420.22731380.19162642X-RAY DIFFRACTION97.68
2.42-2.550.24981410.19722675X-RAY DIFFRACTION97.3
2.55-2.710.23841410.19412675X-RAY DIFFRACTION98.67
2.71-2.920.24531420.19652700X-RAY DIFFRACTION98.82
2.92-3.210.2311420.2012689X-RAY DIFFRACTION97.62
3.21-3.680.22981420.17852703X-RAY DIFFRACTION98.58
3.68-4.630.18231430.14272713X-RAY DIFFRACTION98.31
4.63-38.190.1751430.15472728X-RAY DIFFRACTION97.55
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)
18.198219133150.8996677510765.73550732039.127323439261.247814282019.690893621120.1150603569821.67142548567-0.172522983214-0.9986400692910.3765142645610.2012370216730.150272471177-0.0499436976559-0.5174443639270.5209859964710.03942330600520.006236363806030.758305030560.07684057942390.30657941538518.77963781167.123042496576.64193389775
24.220769945812.316949476010.4140968439645.085189093421.125416092824.22993170323-0.08079000423580.6419682719080.409657189137-0.446525058115-0.0731898998640.66552225201-0.475996284803-0.9058592469750.09787031923980.3711042275910.0861787909323-0.03025255635410.5572060965850.05401781250020.28219900631511.44751825386.5013282795214.8460884457
32.67659310956-0.883515171974-0.2212574500615.253866527382.016444819926.64553893456-0.02084347741010.243465951141-0.0264868268553-0.109966055537-0.01558071757160.211632718747-0.180662967701-0.6858889828440.07069203452710.208855201440.0252475641587-0.03157627839280.3325122104510.05532939035870.19121270190213.37487627962.3975795465622.926115508
45.52946310033-1.3304213145-1.635059114121.72168322293-1.973113691914.492047235420.1126930817820.752075047253-1.67568372579-1.409764244180.2627227224620.4461061749711.28726556238-1.01621323119-0.2717042148531.02199149569-0.1862105763-0.1799096710820.583934807813-0.1356035901010.6339099653913.334632877-18.458910217322.3263333039
52.50733631662-1.0487705698-0.4977651055843.94795633155-1.033551624425.608585373530.0082390954162-0.0780996331598-0.05752813962350.152251883430.1075088982460.250544940930.344507196882-0.391033871465-0.08839855173990.206215556823-0.045716166773-0.0273968721630.273316099950.008759549563270.22556392057417.5012152118-7.2042738923331.3112529457
65.108543699050.197310376831-1.884910725983.39574209089-1.72333799917.644395151770.0346814816358-0.517563789058-0.2486752289250.377409883529-0.105932043568-0.1594068076670.1172842650810.2324195612470.127738242870.2320514104410.0288836477764-0.04131843269130.2345467613850.03680459298650.2262400623925.7772985508-5.3705239488339.5485731352
74.610665357360.00554912868406-2.146554929954.04196140734-0.1906038613793.370803545060.0745347631186-0.3400419927380.2953036274090.6091907324250.0011479416833-0.282882016386-0.2854635041190.0880720743176-0.04805410263710.414720232908-0.0174634252553-0.1066121464810.317114999919-0.02580735106580.33817553233629.20958689277.8104823209941.6862929621
82.77436756691-0.0285977157338-1.325172831053.314943273872.501787828338.863713728870.124127571766-0.1052955439730.2502493275850.217688980149-0.1991860619640.00575698438757-0.714772341011-0.2833264711940.134632440490.4382445956770.0326564161215-0.05261770974860.2641317448750.0003624511747570.33381320444623.001660304613.260778614638.5441695879
96.100061038861.20902626235-4.174255315534.18839437889-3.550498193116.21551052967-0.6759914181321.63161965205-0.1277357773-0.9438827781320.605581729060.007437488882061.09772828931-1.065024022110.115811620251.01656788554-0.3329741941630.09043715599390.648487529688-0.1726992127770.4837113535542.9931588322823.9959925782-14.3606518559
105.044137648041.64348468497-1.677246388145.15826606644-2.931667605163.61112263872-0.5018649717510.280131547441-0.548599128963-0.25605408465-0.143151723216-0.04030293486891.120321264970.3094121803310.5723252141920.644216436974-0.006229414023780.1610208556990.368958568499-0.06305520546540.28199817467410.3714863925.1737016759-6.2909786001
115.02791313637-0.0708378218202-1.157591282894.7726481053-1.046558826694.12249465042-0.395466269229-0.0213669664391-0.2104489487330.1617733200040.04116569847120.03459908150160.7166803334330.1485459706510.2533469118780.3708655763190.03207602134280.08838230798850.1899209873270.005317908810880.2070861717548.2989764371629.98722789721.53354562939
124.484856377931.258832721753.939887059452.212057786272.764754961545.224199087440.04439272987040.5962705264361.03715658767-0.0683656796553-0.195271884853-0.313272648878-1.344153848861.109209690640.08985969374630.761053044558-0.1425031949140.01192613164390.520143831860.1930547348220.5759461255058.0569603091850.6664860184-0.687183981386
133.88803873805-0.91276523712-0.657134054293.276436009881.757858578246.22244857361-0.10583743915-0.1623600710120.08665654711530.09915700502080.0357192376095-0.0279486431353-0.01045466694560.231896839670.08886772221150.215882325509-0.0183792984841-0.01749968717890.1898907128370.03482535234550.178781771244.0341972001440.05237445339.21844620335
146.68390657690.0572736841424-0.9131875731044.957257920760.45672607027.40158179392-0.252260367348-0.3496972366280.1972909439580.3589498540720.006729236669330.2886489907450.0931061333031-0.4429426443570.2356203761440.2663769764650.02790648179870.03971950068980.290839027302-0.02846304414570.286196132712-4.3057670191338.68862476117.5860688373
152.36532018957-0.286829455376-0.1915597513972.56648857979-0.1874564037771.59008823675-0.2967378727-0.397613939943-0.5303451163331.52152606935-0.1502163399730.6431600783621.41020457388-0.5598646172230.2306811518070.970241804476-0.1165022121660.3128864109140.5310673268380.0239596416960.479335875992-7.707993528625.812119221120.5612822054
163.56179833015-1.69912656501-2.407138236454.28779523602-0.9595517149812.89558346161-1.15812927402-0.36951634956-0.5381684885531.397570554910.215311780777-0.1460550650480.8374200413510.1436816922150.8653550543571.16868122649-0.01238877747290.2595647183360.4164600986230.04849937476110.606828575713-1.4451362616620.904630779517.9810074276
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 43 through 61 )AA43 - 611 - 19
22chain 'A' and (resid 62 through 100 )AA62 - 10020 - 58
33chain 'A' and (resid 101 through 147 )AA101 - 14759 - 105
44chain 'A' and (resid 148 through 169 )AA148 - 169106 - 127
55chain 'A' and (resid 170 through 215 )AA170 - 215128 - 173
66chain 'A' and (resid 216 through 253 )AA216 - 253174 - 211
77chain 'A' and (resid 254 through 294 )AA254 - 294212 - 252
88chain 'A' and (resid 295 through 321 )AA295 - 321253 - 279
99chain 'B' and (resid 43 through 61 )BC43 - 611 - 19
1010chain 'B' and (resid 62 through 100 )BC62 - 10020 - 58
1111chain 'B' and (resid 101 through 147 )BC101 - 14759 - 105
1212chain 'B' and (resid 148 through 169 )BC148 - 169106 - 127
1313chain 'B' and (resid 170 through 215 )BC170 - 215128 - 173
1414chain 'B' and (resid 216 through 253 )BC216 - 253174 - 211
1515chain 'B' and (resid 254 through 294 )BC254 - 294212 - 252
1616chain 'B' and (resid 295 through 321 )BC295 - 321253 - 279

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