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- PDB-8hkb: TPA bound-form of Periplasmic terephthalate binding protein (TBP)... -

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Basic information

Entry
Database: PDB / ID: 8hkb
TitleTPA bound-form of Periplasmic terephthalate binding protein (TBP) from Ideonella sakaiensis mutant K184D
ComponentsPeriplasmic terephthalate binding protein (TBP)
KeywordsTRANSPORT PROTEIN / Periplasmic protein / Terephthalate binding protein / transportation protein / Ideonella sakaiensis
Function / homologyBordetella uptake gene / Bordetella uptake gene, domain 1 / Tripartite tricarboxylate transporter family receptor / terephthalic acid / Putative exported protein
Function and homology information
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLee, S.H. / Seo, H. / Kim, K.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Molecular mechanism underlying high-affinity terephthalate binding and conformational change of TBP from Ideonella sakaiensis.
Authors: Lee, S.H. / Seo, H. / Hong, H. / Kim, M. / Kim, K.J.
History
DepositionNov 25, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic terephthalate binding protein (TBP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8702
Polymers32,7041
Non-polymers1661
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size-exclusive liquid chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.054, 59.302, 54.298
Angle α, β, γ (deg.)90.00, 104.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic terephthalate binding protein (TBP)


Mass: 32704.191 Da / Num. of mol.: 1 / Mutation: K184D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Strain: NBRC 110686 / TISTR 2288 / 201-F6 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K8P8D2
#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.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 25 % PEG3350 and 0.2 M Ammonium citrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 48172 / % possible obs: 99 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.078 / Χ2: 0.069 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.4-1.421.60.68823741.936198.5
1.42-1.451.60.6323672.192198.6
1.45-1.481.60.55824022.319199
1.48-1.511.60.48423922.452198.6
1.51-1.541.60.39124062.698198.7
1.54-1.581.70.3523852.95199
1.58-1.621.70.28923832.924198.8
1.62-1.661.70.26124122.942199.4
1.66-1.711.70.23824233.274199.4
1.71-1.761.70.20323973.372199.3
1.76-1.831.70.17524123.798199.4
1.83-1.91.70.15324224.076199.3
1.9-1.991.80.13824224.619199.5
1.99-2.091.80.11724154.919199.6
2.09-2.221.80.11224345.497199.7
2.22-2.391.90.09824125.637199.5
2.39-2.631.90.08724285.527199.8
2.63-3.021.90.07824565.692199.9
3.02-3.81.90.06724475.954199.4
3.8-501.80.06623836.363194.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC8refinement
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→28.12 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.881 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18061 2403 5 %RANDOM
Rwork0.15273 ---
obs0.15413 45754 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.329 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0.43 Å2
2--0.61 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.4→28.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 12 300 2593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162156
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.653218
X-RAY DIFFRACTIONr_angle_other_deg0.6041.5575025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4385301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.034514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6710348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02447
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4691.261207
X-RAY DIFFRACTIONr_mcbond_other1.4691.261207
X-RAY DIFFRACTIONr_mcangle_it2.2381.8851507
X-RAY DIFFRACTIONr_mcangle_other2.2381.8881508
X-RAY DIFFRACTIONr_scbond_it2.6171.5671147
X-RAY DIFFRACTIONr_scbond_other2.6211.571144
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8422.2311710
X-RAY DIFFRACTIONr_long_range_B_refined5.19323.5752639
X-RAY DIFFRACTIONr_long_range_B_other4.92820.1972561
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.435 Å
RfactorNum. reflection% reflection
Rfree0.207 162 -
Rwork0.185 3283 -
obs--95.91 %

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