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- PDB-4jb0: Rhodopseudomonas palustris (strain CGA009) Rp1789 transport protein -

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Basic information

Entry
Database: PDB / ID: 4jb0
TitleRhodopseudomonas palustris (strain CGA009) Rp1789 transport protein
Componentsbranched-chain amino acid transport system substrate-binding protein
KeywordsTRANSPORT PROTEIN / aromatic lignin binding transport / ABC transport system binding protein / Bind small aromatic ligands from lignin degradation
Function / homology
Function and homology information


amino acid transport
Similarity search - Function
: / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(4-HYDROXY-PHENYL)PYRUVIC ACID / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsSalmon, R.
CitationJournal: Plos One / Year: 2013
Title: The CouPSTU and TarPQM Transporters in Rhodopseudomonas palustris: Redundant, Promiscuous Uptake Systems for Lignin-Derived Aromatic Substrates.
Authors: Salmon, R.C. / Cliff, M.J. / Rafferty, J.B. / Kelly, D.J.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: branched-chain amino acid transport system substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2124
Polymers39,7451
Non-polymers4663
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.970, 70.740, 105.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein branched-chain amino acid transport system substrate-binding protein


Mass: 39745.223 Da / Num. of mol.: 1 / Fragment: Aromatic compound transport protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: 1789 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6N8W4
#2: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 1 / Fragment: Aromatic Ligand / Source method: obtained synthetically / Formula: C10H10O4
#3: Chemical ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP


Mass: 180.157 Da / Num. of mol.: 1 / Fragment: Aromatic Ligand / Source method: obtained synthetically / Formula: C9H8O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 176 / Fragment: Solvent component / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate, pH 4.5, 25% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2012
RadiationMonochromator: Si channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.91→44.3 Å / Num. all: 46986 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3
Reflection shellResolution: 1.91→1.96 Å / Mean I/σ(I) obs: 1.6 / Num. unique all: 3551 / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→42.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.547 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1295 5.1 %RANDOM
Rwork0.17609 ---
obs0.17876 24165 100 %-
all-46986 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.307 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2--0.88 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.91→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 33 176 2970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222848
X-RAY DIFFRACTIONr_angle_refined_deg1.681.983864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90824.182110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80815469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2621516
X-RAY DIFFRACTIONr_chiral_restr0.1130.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212145
X-RAY DIFFRACTIONr_mcbond_it0.9671.51826
X-RAY DIFFRACTIONr_mcangle_it1.61622937
X-RAY DIFFRACTIONr_scbond_it2.64631022
X-RAY DIFFRACTIONr_scangle_it4.0154.5927
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 101 -
Rwork0.24 1769 -
obs--100 %

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