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- PDB-5oku: R. palustris Rpa4515 with adipate -

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Basic information

Entry
Database: PDB / ID: 5oku
TitleR. palustris Rpa4515 with adipate
ComponentsUncharacterized protein family UPF0065:Tat pathway signal
KeywordsTRANSPORT PROTEIN / Tripartite tricarboxylate transporter
Function / homologyBordetella uptake gene / Bordetella uptake gene, domain 1 / Tripartite tricarboxylate transporter family receptor / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / hexanedioic acid / ACETIC ACID / Tripartite tricarboxylate transporter substrate binding protein
Function and homology information
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsRosa, L. / Rafferty, J. / Kelly, D. / Dix, S.R.
CitationJournal: FEBS J. / Year: 2017
Title: Structural basis for high-affinity adipate binding to AdpC (RPA4515), an orphan periplasmic-binding protein from the tripartite tricarboxylate transporter (TTT) family in Rhodopseudomonas palustris.
Authors: Rosa, L.T. / Dix, S.R. / Rafferty, J.B. / Kelly, D.J.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein family UPF0065:Tat pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4008
Polymers35,7211
Non-polymers6797
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-40 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.900, 166.609, 82.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein family UPF0065:Tat pathway signal / rpa4515


Mass: 35721.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Gene: RPA4515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N193

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Non-polymers , 5 types, 108 molecules

#2: Chemical ChemComp-0L1 / hexanedioic acid / Adipic acid


Mass: 146.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 5 / Details: ammonium sulphate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.07→41.65 Å / Num. obs: 20144 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.977 / Rmerge(I) obs: 0.63 / Rpim(I) all: 0.21 / Rrim(I) all: 0.67 / Net I/σ(I): 5
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 2.59 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1010 / CC1/2: 0.49 / Rpim(I) all: 0.9 / Rsym value: 2.76 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qpq

2qpq


Resolution: 2.07→41.65 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.684 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.188 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 998 5 %RANDOM
Rwork0.20732 ---
obs0.20965 19116 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.362 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--2.27 Å20 Å2
3----1.71 Å2
Refinement stepCycle: 1 / Resolution: 2.07→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 41 101 2379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192324
X-RAY DIFFRACTIONr_bond_other_d0.0020.022191
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.9833173
X-RAY DIFFRACTIONr_angle_other_deg1.03935062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21922.22281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34215348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8521518
X-RAY DIFFRACTIONr_chiral_restr0.1030.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212559
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02459
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_it1.4811.9641196
X-RAY DIFFRACTIONr_mcbond_other1.4681.961194
X-RAY DIFFRACTIONr_mcangle_it2.2992.9341492
X-RAY DIFFRACTIONr_mcangle_other2.3062.9361493
X-RAY DIFFRACTIONr_scbond_it2.3172.3381127
X-RAY DIFFRACTIONr_scbond_other2.3162.3391128
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7023.3741682
X-RAY DIFFRACTIONr_long_range_B_refined5.36624.4532596
X-RAY DIFFRACTIONr_long_range_B_other5.36424.4522596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 77 -
Rwork0.327 1398 -
obs--99.93 %

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