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- PDB-8g53: Crystal structure of a bacterial TPAT family transporter -

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Basic information

Entry
Database: PDB / ID: 8g53
TitleCrystal structure of a bacterial TPAT family transporter
ComponentsTPR_REGION domain-containing protein
KeywordsLIPID BINDING PROTEIN / Transporter / sterols
Function / homologyTetratricopeptide-like helical domain superfamily / Tetratricopeptide repeat protein
Function and homology information
Biological speciesEnhygromyxa salina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TPR_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)22,5981
Polymers22,5981
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.945, 59.029, 62.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein TPR_REGION domain-containing protein


Mass: 22598.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enhygromyxa salina (bacteria) / Gene: DB30_08039 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0C1ZR44
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Sulfate 0.1 M Tris: HCl, pH 8.5 1.26 M Ammonium Sulfate

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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: Oct 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.03→33.34 Å / Num. obs: 91316 / % possible obs: 93.73 % / Redundancy: 8.3 % / Biso Wilson estimate: 10.92 Å2 / CC1/2: 0.999 / Net I/σ(I): 26.55
Reflection shellResolution: 1.03→1.067 Å / Num. unique obs: 5924 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→33.34 Å / SU ML: 0.0971 / Cross valid method: FREE R-VALUE / Phase error: 17.1228
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1829 4564 5 %
Rwork0.1651 86941 -
obs-91316 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.51 Å2
Refinement stepCycle: LAST / Resolution: 1.03→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 0 330 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01021376
X-RAY DIFFRACTIONf_angle_d1.0591868
X-RAY DIFFRACTIONf_chiral_restr0.0778213
X-RAY DIFFRACTIONf_plane_restr0.0118253
X-RAY DIFFRACTIONf_dihedral_angle_d4.3865202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.040.3236760.32941450X-RAY DIFFRACTION47.72
1.04-1.050.2853990.2781874X-RAY DIFFRACTION60.84
1.05-1.060.28861100.25442094X-RAY DIFFRACTION67.92
1.06-1.080.24281250.23062379X-RAY DIFFRACTION77.4
1.08-1.090.20221360.2052582X-RAY DIFFRACTION84.73
1.09-1.110.22621500.19712829X-RAY DIFFRACTION91.49
1.11-1.120.2031560.18412963X-RAY DIFFRACTION96.06
1.12-1.140.16941560.18072970X-RAY DIFFRACTION97.14
1.14-1.160.18141580.1752992X-RAY DIFFRACTION97.4
1.16-1.180.1791590.17313027X-RAY DIFFRACTION98.09
1.18-1.20.18231570.17952978X-RAY DIFFRACTION97.79
1.2-1.220.18561610.18213051X-RAY DIFFRACTION98.47
1.22-1.240.18181590.19253022X-RAY DIFFRACTION98.36
1.24-1.270.21321610.17423051X-RAY DIFFRACTION98.44
1.27-1.290.17381600.16433050X-RAY DIFFRACTION98.8
1.29-1.320.16491610.15753057X-RAY DIFFRACTION98.83
1.32-1.360.19941600.15913042X-RAY DIFFRACTION98.67
1.36-1.390.19661620.15663070X-RAY DIFFRACTION98.87
1.39-1.440.16911600.16053041X-RAY DIFFRACTION98.25
1.44-1.480.15411620.15233078X-RAY DIFFRACTION99.42
1.48-1.530.15751610.15343054X-RAY DIFFRACTION99.35
1.53-1.60.14591640.14663132X-RAY DIFFRACTION99.67
1.6-1.670.14661620.14553067X-RAY DIFFRACTION99.35
1.67-1.760.17481620.15723077X-RAY DIFFRACTION97.88
1.76-1.870.18171630.16063099X-RAY DIFFRACTION99.57
1.87-2.010.21081640.16353119X-RAY DIFFRACTION99.85
2.01-2.210.17951660.15223162X-RAY DIFFRACTION99.85
2.21-2.530.16531650.15363131X-RAY DIFFRACTION98.86
2.53-3.190.19291680.16933183X-RAY DIFFRACTION99.67
3.19-33.340.18891740.17053317X-RAY DIFFRACTION99.09
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)
12.363634048161.22880645908-1.746183788311.45116081147-1.516461037332.136993241880.02390113269780.1558244451730.09417047262880.009531492073220.07997326070640.0481710720872-0.0183936044327-0.0561746543584-0.08572572458280.119562801497-0.02248607007760.007942229205350.115496321417-0.003595249954240.0894430216594-2.557780655968.0453346626118.4634526905
20.4816961734760.167794015466-1.146492783760.733331881508-0.8213375982794.678756028580.07853191722060.002805807141250.1088740196330.0370217754875-0.005242529802850.0109062921571-0.298896466102-0.0036928205037-0.07625983767110.122834452918-0.008382206181830.00533949198620.0971290051242-0.0007284892814460.118898461589-10.230639132112.764549072218.6254496578
34.02829308413-1.84820073129-1.394290334073.96555325684.013470591854.134067759250.02185848089930.2496664499280.049284717364-0.4505560012250.0509495441423-0.177592774106-0.3644452005050.0836247288162-0.03095193758970.150985316463-0.03980656889050.004484983040840.1474413322050.008440402251240.119447474892-0.09385052618749.929848451472.92759015781
43.04568490539-0.849922812804-0.8493043972170.6441678584340.2451280220411.41424582011-0.0360644545663-0.0756791817054-0.133496360726-0.013340601026-0.005485991829840.0998954140095-0.091461843899-0.003009460305060.03901562000990.0974139742393-0.00144337007302-0.01114952116810.0848568658787-0.001545369840890.102191625185-12.90217755995.8291498650112.5179682894
53.40760202745-0.41830745903-0.6496426190231.562411128750.4857016332891.54764483324-0.05014392755440.05327924140770.0056227169932-0.0693045706220.003776850339830.0770851032794-0.0999677870435-0.02435647983180.03864068599550.104448624471-0.00578642677028-0.01203118784540.08720538291530.001065834229740.0735585407186-11.97255561633.774065237493.35446355653
62.73929929842-0.3197654357530.1111442961911.661263467240.1309309753051.189739929660.03968380320590.04597114587930.0542644172983-0.0920344313285-0.038800615640.0855059945186-0.0271330596724-0.0544098341516-0.00597853728320.08926354933170.00356736385981-0.001897325435960.06812161396630.003848447856370.081496554674-15.8501005004-3.083096331486.73810585226
73.82638362163-1.592356728461.082973515553.88183449907-0.9609666014273.503678043720.01206539453780.168240003963-0.0557549236614-0.1461066256720.02658247024630.2310610372890.225310408889-0.169191810337-0.03048275233760.122226338619-0.00766544028108-0.0108749145610.09282118691160.001729727482310.0846115315177-16.3975290534-12.00946614564.47663279889
84.00373685964-0.687968533984-0.5794348907561.494595496380.01151365409231.41564825663-0.045782240239-0.0497787668088-0.0207034839706-0.02715027386940.04081872499270.01881996568040.109896067655-0.0002809051702760.0007573276812810.09501608251330.00160004099363-0.0009210085051910.08103742957750.004789388481610.080924271673-13.7259735306-13.51833261113.3053846877
92.063957897820.3109763017140.309072602370.9084085103990.103517448550.8903452038040.0029233333843-0.00189226496699-0.22552465390.01591053322630.02191274343150.07293322871250.163905656152-0.0998147844191-0.02222305191520.104107809018-0.01319327318680.005608800947180.09089666560893.06112846114E-50.118587778615-16.1246948008-17.692623914618.0271926736
104.167367197632.37568959128-0.4561046707963.33731686188-0.1048886843552.123801240390.07935301408630.05905303110330.1722603553240.131184165531-0.02338308596880.3028226053470.114018850896-0.258394596169-0.05101835113990.101666913434-0.01143913840420.01365880269090.1161957013-0.003938337402950.101872993885-16.7269682699-10.304301434324.4047590937
117.25123278443-3.43143564157-0.09145333392446.693581972550.9498649696881.170101656260.270315292729-0.573777101836-0.2260353737620.613387428283-0.52409202534-0.3872881033470.08623936352420.04526701155910.2466392072750.222386104988-0.134128369706-0.04246273618360.3049057118380.1162334324110.278387219267-21.7047922747-22.324097862425.5313103692
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 29 through 47 )29 - 471 - 19
22chain 'A' and (resid 48 through 64 )48 - 6420 - 36
33chain 'A' and (resid 65 through 70 )65 - 7037 - 42
44chain 'A' and (resid 71 through 92 )71 - 9243 - 64
55chain 'A' and (resid 93 through 112 )93 - 11265 - 84
66chain 'A' and (resid 113 through 137 )113 - 13785 - 109
77chain 'A' and (resid 138 through 151 )138 - 151110 - 123
88chain 'A' and (resid 152 through 168 )152 - 168124 - 140
99chain 'A' and (resid 169 through 190 )169 - 190141 - 162
1010chain 'A' and (resid 191 through 203 )191 - 203163 - 175
1111chain 'A' and (resid 204 through 212 )204 - 212176 - 184

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