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- PDB-4fb4: The Structure of an ABC-Transporter Family Protein from Rhodopseu... -

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Basic information

Entry
Database: PDB / ID: 4fb4
TitleThe Structure of an ABC-Transporter Family Protein from Rhodopseudomonas palustris in Complex with Caffeic Acid
ComponentsPutative branched-chain amino acid transport system substrate-binding protein
KeywordsSIGNALING PROTEIN / Structural Genomics / PSI-Biology / alpha/beta / aromatic compound transport / aromatic compounds / Midwest Center for Structural Genomics / MCSG
Function / homologyLeucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CAFFEIC ACID / Branched-chain amino acid transport system substrate-binding protein
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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
DepositionMay 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: 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 15, 2017Group: Refinement description / Category: software

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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)39,4273
Polymers39,1551
Non-polymers2722
Water2,288127
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.986, 71.055, 91.015
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

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


Mass: 39155.152 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID / Caffeic acid


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


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


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES:NaOH pH 6.5, 30% PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionRedundancy: 7.8 % / Av σ(I) over netI: 22.29 / Number: 215442 / Rmerge(I) obs: 0.085 / Χ2: 0.92 / D res high: 1.85 Å / D res low: 50 Å / Num. obs: 27597 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.025098.110.0480.6597
3.995.0299.710.0520.7997.3
3.483.9999.510.0580.9787.6
3.163.4899.610.0681.0497.8
2.943.1699.610.081.0237.9
2.762.9499.410.0881.0058
2.632.7699.310.1030.9838
2.512.6399.110.1180.9628
2.412.5198.810.1330.9318
2.332.4199.710.1560.9348
2.262.3398.910.1840.9728
2.192.2698.210.2150.9528
2.142.1910010.240.9338.1
2.082.1497.910.290.9218
2.042.0899.210.3460.9178
1.992.0498.110.4180.9217.9
1.951.9998.910.4370.8467.9
1.921.9597.610.580.8497.7
1.881.9299.310.6510.8577.6
1.851.8896.610.6840.8037.5
ReflectionResolution: 1.85→50 Å / Num. all: 27597 / Num. obs: 27597 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.085 / Χ2: 0.917 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.887.50.68413430.803196.6
1.88-1.927.60.65113520.857199.3
1.92-1.957.70.5813300.849197.6
1.95-1.997.90.43713590.846198.9
1.99-2.047.90.41813410.921198.1
2.04-2.0880.34613520.917199.2
2.08-2.1480.2913570.921197.9
2.14-2.198.10.2413750.9331100
2.19-2.2680.21513470.952198.2
2.26-2.3380.18413750.972198.9
2.33-2.4180.15613700.934199.7
2.41-2.5180.13313770.931198.8
2.51-2.6380.11813670.962199.1
2.63-2.7680.10313830.983199.3
2.76-2.9480.08813881.005199.4
2.94-3.167.90.0813901.023199.6
3.16-3.487.80.06814181.049199.6
3.48-3.997.60.05814220.978199.5
3.99-5.027.30.05214420.799199.7
5.02-5070.04815090.659198.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.36 Å / D res low: 50 Å / FOM : 0.278 / FOM acentric: 0.324 / FOM centric: 0 / Reflection: 13542 / Reflection acentric: 11622 / Reflection centric: 1920
Phasing MAD setR cullis acentric: 1.52 / R cullis centric: 1 / Highest resolution: 2.36 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 11622 / Reflection centric: 1920
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
14.19-502.210.50.23338
8.27-14.191.320.40.317792
5.83-8.271.980.40.2457161
4.51-5.831.330.20.2867218
3.67-4.511.160.20.11404273
3.1-3.671.340.10.12062324
2.68-3.11.840.102856380
2.36-2.682.330.103766434
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
144.0586-0.112-0.856-0.1496.244
241.48250.189-1-0.2775.202
335.68170.076-0.853-0.2664.011
437.86390.12-0.972-0.2054.047
537.70910.31-0.8-0.3452.511
645.07380.466-0.819-0.3362.31
775.5197-0.16-0.777-0.2123.949
863.62990.196-1.089-0.232.163
981.569-0.02-0.994-0.321.959
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
14.19-500.1780.3830713338
8.27-14.190.2840.431026917792
5.83-8.270.3950.5340618457161
4.51-5.830.3840.4801085867218
3.67-4.510.3420.408016771404273
3.1-3.670.3280.38023862062324
2.68-3.10.2540.288032362856380
2.36-2.680.1980.221042003766434
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 27132
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.25-100650.686502
5.73-7.2564.60.808509
4.98-5.7363.30.816520
4.46-4.9863.10.851572
4.07-4.4665.40.849641
3.77-4.0767.10.835690
3.53-3.77670.821727
3.33-3.5367.70.801781
3.16-3.3367.80.784827
3.02-3.1673.60.748845
2.89-3.0272.20.733890
2.78-2.8971.40.73926
2.67-2.7870.50.72952
2.58-2.6773.30.687994
2.5-2.5874.40.7211040
2.43-2.573.60.6811036
2.36-2.4377.50.6871093
2.3-2.3689.60.6751093
2.24-2.390.60.6681151
2.19-2.2490.90.6691164
2.14-2.1992.20.6421188
2.09-2.14910.6351203
2.04-2.0989.10.5941257
2-2.0491.30.5951254
1.96-287.70.5371276
1.93-1.9688.80.5271299
1.89-1.9389.70.5031350
1.85-1.8992.20.3961352

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→35.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2184 / WRfactor Rwork: 0.1689 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8801 / SU B: 5.9 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1516 / SU Rfree: 0.1417 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.142
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 1290 5.1 %RANDOM
Rwork0.1661 ---
all0.1685 25528 --
obs0.1685 25528 91.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.85 Å2 / Biso mean: 24.1958 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 19 127 2845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022774
X-RAY DIFFRACTIONr_bond_other_d0.0020.021872
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9823766
X-RAY DIFFRACTIONr_angle_other_deg1.03634596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5375361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80124.286105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59415463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.611516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213091
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02525
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 44 -
Rwork0.182 1181 -
all-1225 -
obs--63.31 %
Refinement TLS params.Method: refined / Origin x: 11.9476 Å / Origin y: 60.1327 Å / Origin z: 22.4573 Å
111213212223313233
T0.0107 Å20.0031 Å2-0.0044 Å2-0.0177 Å2-0.0156 Å2--0.0275 Å2
L0.6596 °20.227 °20.1868 °2-1.2836 °20.5146 °2--0.9563 °2
S0.0185 Å °-0.0627 Å °0.0147 Å °0.0617 Å °0.0519 Å °-0.1527 Å °-0.0151 Å °0.04 Å °-0.0705 Å °

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