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- PDB-5oei: R. palustris Rpa4515 with oxoadipate -

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Basic information

Entry
Database: PDB / ID: 5oei
TitleR. palustris Rpa4515 with oxoadipate
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 / 2-OXOADIPIC ACID / Tripartite tricarboxylate transporter substrate binding protein
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 7, 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 1.2Mar 14, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 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)36,4548
Polymers35,7211
Non-polymers7337
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-49 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.314, 168.468, 82.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 35721.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA4515 / Plasmid: pBAD-HisB / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 (DE3) / References: UniProt: Q6N193
#2: Chemical ChemComp-OOG / 2-OXOADIPIC ACID


Mass: 160.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 5 / Details: 2 M ammmonium sulphate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.78→59 Å / Num. obs: 32168 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.95 / Num. unique obs: 1594 / Rpim(I) all: 0.53 / Χ2: 0.572 / % possible all: 99.6

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Processing

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

2qpq


Resolution: 1.78→59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.68 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 1671 5.2 %RANDOM
Rwork0.1809 ---
obs0.18276 30497 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--1.39 Å20 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.78→59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 42 111 2395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192330
X-RAY DIFFRACTIONr_bond_other_d0.0010.022187
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9853185
X-RAY DIFFRACTIONr_angle_other_deg1.0535056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12322.31782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98715351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3121518
X-RAY DIFFRACTIONr_chiral_restr0.1140.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
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_it1.5121.6881196
X-RAY DIFFRACTIONr_mcbond_other1.5121.6871195
X-RAY DIFFRACTIONr_mcangle_it2.0752.521492
X-RAY DIFFRACTIONr_mcangle_other2.0742.5221493
X-RAY DIFFRACTIONr_scbond_it2.6482.0561132
X-RAY DIFFRACTIONr_scbond_other2.6422.0561132
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9082.961694
X-RAY DIFFRACTIONr_long_range_B_refined5.44320.7122412
X-RAY DIFFRACTIONr_long_range_B_other5.43820.7132412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 112 -
Rwork0.293 2253 -
obs--100 %

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