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- PDB-4jb2: Rhodopseudomonas palustris (strain CGA009) Rp1789 -

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Basic information

Entry
Database: PDB / ID: 4jb2
TitleRhodopseudomonas palustris (strain CGA009) Rp1789
ComponentsBranched-chain amino acid transport system substrate-binding protein
KeywordsTRANSPORT PROTEIN / lignin binding / ABC Transport system / substrate binding protein
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
ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)40,1145
Polymers39,7451
Non-polymers3684
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.930, 66.430, 100.520
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
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.8 Å3/Da / Density % sol: 31.79 %
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 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→43 Å / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3
Reflection shellResolution: 2.1→2.15 Å / Num. unique all: 2389 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.08 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.823 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22769 879 5.1 %RANDOM
Rwork0.17411 ---
obs0.17686 16463 100 %-
all-17343 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.393 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å20 Å2
2--2.12 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 24 67 2747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222730
X-RAY DIFFRACTIONr_angle_refined_deg1.811.983705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83524.175103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4315441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3621516
X-RAY DIFFRACTIONr_chiral_restr0.120.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212036
X-RAY DIFFRACTIONr_mcbond_it0.9081.51776
X-RAY DIFFRACTIONr_mcangle_it1.58622853
X-RAY DIFFRACTIONr_scbond_it2.8143954
X-RAY DIFFRACTIONr_scangle_it4.514.5852
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 61 -
Rwork0.246 1201 -
obs--100 %

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