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- PDB-7nds: Crystal structure of TphC in a closed conformation -

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Basic information

Entry
Database: PDB / ID: 7nds
TitleCrystal structure of TphC in a closed conformation
ComponentsTripartite tricarboxylate transporter substrate binding protein
KeywordsTRANSPORT PROTEIN / Solute binding protein
Function / homologyBordetella uptake gene / Bordetella uptake gene, domain 1 / Tripartite tricarboxylate transporter family receptor / terephthalic acid / Tripartite tricarboxylate transporter substrate binding protein
Function and homology information
Biological speciesComamonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLevy, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Commonwealth Scholarship Commission (United Kingdom)INCN-2018-57 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of terephthalate recognition by solute binding protein TphC.
Authors: Gautom, T. / Dheeman, D. / Levy, C. / Butterfield, T. / Alvarez Gonzalez, G. / Le Roy, P. / Caiger, L. / Fisher, K. / Johannissen, L. / Dixon, N.
History
DepositionFeb 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _audit_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite tricarboxylate transporter substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9592
Polymers33,7931
Non-polymers1661
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.250, 150.060, 58.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

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Components

#1: Protein Tripartite tricarboxylate transporter substrate binding protein


Mass: 33792.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas sp. (bacteria) / Gene: E2578_22390 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5N7XFM8
#2: Chemical ChemComp-UB7 / terephthalic acid / benzene-1,4-dicarboxylic acid


Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 0.1M MES pH 6.5, 30% w/v PEG 5000 MME condition SG1 drop B4
Temp details: Incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→46.17 Å / Num. obs: 12237 / % possible obs: 99.25 % / Redundancy: 6.6 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1682 / Rpim(I) all: 0.07 / Rrim(I) all: 0.1825 / Net I/σ(I): 9.37
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 6 % / Rmerge(I) obs: 1.057 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1172 / CC1/2: 0.505 / CC star: 0.819 / Rpim(I) all: 0.4617 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X9T

4x9t


Resolution: 2.4→46.17 Å / SU ML: 0.2824 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.025
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 620 5.07 %
Rwork0.1785 11617 -
obs0.1805 12237 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.59 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 12 130 2361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252283
X-RAY DIFFRACTIONf_angle_d0.52853114
X-RAY DIFFRACTIONf_chiral_restr0.0452360
X-RAY DIFFRACTIONf_plane_restr0.0045405
X-RAY DIFFRACTIONf_dihedral_angle_d14.405834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.27531570.24142810X-RAY DIFFRACTION98.47
2.64-3.020.2391370.21842895X-RAY DIFFRACTION99.38
3.02-3.810.2261400.17772915X-RAY DIFFRACTION99.64
3.81-46.170.19421860.14852997X-RAY DIFFRACTION99.59

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