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- PDB-3tx6: The Structure of a putative ABC-transporter periplasmic component... -

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Basic information

Entry
Database: PDB / ID: 3tx6
TitleThe Structure of a putative ABC-transporter periplasmic component from Rhodopseudomonas palustris
ComponentsPutative branched-chain amino acid transport system substrate-binding protein
KeywordsSIGNALING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / putative branched-chain amino acid
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
ACETIC ACID / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsCuff, M.E. / Mack, J.C. / Zerbs, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2013
Title: Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-Coumaric acid and related aromatic acids.
Authors: Tan, K. / Chang, C. / Cuff, M. / Osipiuk, J. / Landorf, E. / Mack, J.C. / Zerbs, S. / Joachimiak, A. / Collart, F.R.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Aug 7, 2013Group: Database references
Revision 1.4Sep 25, 2013Group: Database references
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Revision 1.6Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Putative branched-chain amino acid transport system substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6857
Polymers39,1551
Non-polymers5306
Water7,206400
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.564, 68.668, 90.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 39155.152 Da / Num. of mol.: 1 / Fragment: UNP residues 27-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: LivK, RPA1789 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q6N8W4

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Non-polymers , 6 types, 406 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 1.93 Å3/Da / Density % sol: 36.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris Propane:NaOH pH 7.0, 2.5M Amonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921, 0.97935
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979351
ReflectionResolution: 1.5→50 Å / Num. all: 49224 / Num. obs: 49224 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.075 / Χ2: 2.427 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.537.90.45924640.619199.9
1.53-1.558.60.40223750.615199.5
1.55-1.588.50.35924560.6591100
1.58-1.628.60.29924280.68199.9
1.62-1.658.60.26224230.727199.8
1.65-1.698.60.21924200.8071100
1.69-1.738.60.19324420.874199.9
1.73-1.788.60.16724330.935199.9
1.78-1.838.70.14324311.074199.9
1.83-1.898.70.12224481.3199.9
1.89-1.968.70.1124531.511100
1.96-2.048.80.09724471.851100
2.04-2.138.80.08824602.2211100
2.13-2.248.80.0824432.5431100
2.24-2.388.90.0824902.9921100
2.38-2.568.90.08124663.8051100
2.56-2.828.80.0824954.6151100
2.82-3.238.70.07225225.4271100
3.23-4.078.50.05625215.617199.7
4.07-5080.06226079.22197.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2019 / WRfactor Rwork: 0.1391 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9162 / SU B: 2.984 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0938 / SU Rfree: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.081
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 2483 5.1 %RANDOM
Rwork0.137 ---
all0.14 49034 --
obs0.14 49034 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.18 Å2 / Biso mean: 24.7198 Å2 / Biso min: 9.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--0.3 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 32 400 3135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192992
X-RAY DIFFRACTIONr_bond_other_d0.0010.022021
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9994087
X-RAY DIFFRACTIONr_angle_other_deg0.99734971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20824.188117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54715473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6421520
X-RAY DIFFRACTIONr_chiral_restr0.1020.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02579
X-RAY DIFFRACTIONr_rigid_bond_restr4.135013
X-RAY DIFFRACTIONr_sphericity_free42.23584
X-RAY DIFFRACTIONr_sphericity_bonded16.17655262
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 168 -
Rwork0.143 3149 -
all-3317 -
obs--97.93 %

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