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

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Basic information

Entry
Database: PDB / ID: 8hka
TitleTPA bound-form of Periplasmic terephthalate binding protein (TBP) from Ideonella sakaiensis
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: 1.02 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)33,2382
Polymers33,0721
Non-polymers1661
Water5,260292
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)46.182, 54.101, 50.600
Angle α, β, γ (deg.)90.00, 104.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic terephthalate binding protein (TBP)


Mass: 33071.633 Da / Num. of mol.: 1
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.: 292 / 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: 1.91 Å3/Da / Density % sol: 35.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG3350 and 0.2 M Ammonium iodide

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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: Apr 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.02→50 Å / Num. obs: 122150 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Χ2: 0.051 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.02-1.043.30.74460821.267199.9
1.04-1.063.40.62161211.372199.8
1.06-1.083.50.51761281.441199.8
1.08-1.13.50.42160851.53199.9
1.1-1.123.50.37360871.632199.8
1.12-1.153.60.30761201.734199.9
1.15-1.183.60.27461211.828199.8
1.18-1.213.60.2560911.867199.8
1.21-1.243.60.22660841.906199.8
1.24-1.293.60.20261431.906199.8
1.29-1.333.60.18360851.925199.8
1.33-1.383.70.1661442.061199.8
1.38-1.453.70.14161462.188199.8
1.45-1.523.70.11760962.282199.8
1.52-1.623.70.10361332.423199.8
1.62-1.743.70.09361552.563199.8
1.74-1.923.70.08461532.795199.8
1.92-2.23.60.07461522.973199.8
2.2-2.773.60.06861643.049199.8
2.77-503.10.06558603.434190.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC8refinement
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→20.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 0.442 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22927 6204 5.1 %RANDOM
Rwork0.20441 ---
obs0.20567 115894 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å2-0.5 Å2
2--0.02 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.02→20.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 12 292 2554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122327
X-RAY DIFFRACTIONr_bond_other_d0.0070.0162267
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.6553177
X-RAY DIFFRACTIONr_angle_other_deg0.6151.5745164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.315298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.727514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96810350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
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_it1.1331.0121198
X-RAY DIFFRACTIONr_mcbond_other1.1211.0041195
X-RAY DIFFRACTIONr_mcangle_it1.5861.521494
X-RAY DIFFRACTIONr_mcangle_other1.5771.5151493
X-RAY DIFFRACTIONr_scbond_it2.0311.251129
X-RAY DIFFRACTIONr_scbond_other2.0281.2481114
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0491.771662
X-RAY DIFFRACTIONr_long_range_B_refined4.55326.1552743
X-RAY DIFFRACTIONr_long_range_B_other4.25923.5752623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.02→1.045 Å
RfactorNum. reflection% reflection
Rfree0.336 442 -
Rwork0.327 8332 -
obs--97.04 %

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