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- PDB-4f8j: The structure of an aromatic compound transport protein from Rhod... -

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Basic information

Entry
Database: PDB / ID: 4f8j
TitleThe structure of an aromatic compound transport protein from Rhodopseudomonas palustris in complex with p-coumarate
ComponentsPutative branched-chain amino acid transport system substrate-binding protein
KeywordsSIGNALING PROTEIN / lignin degratation / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha/beta
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
4'-HYDROXYCINNAMIC ACID / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 17, 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
Revision 1.6Mar 26, 2025Group: 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

Downloads & links

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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)40,25411
Polymers39,1551
Non-polymers1,09810
Water6,954386
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.872, 69.012, 91.307
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
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, 396 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 386 / 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: 1.97 Å3/Da / Density % sol: 37.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES: NaOH pH 7.5, 2M ammonium sulfate, p-coumarate, 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 2, 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: 10.3 % / Av σ(I) over netI: 42.8 / Number: 428255 / Rmerge(I) obs: 0.081 / Χ2: 1.9 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 41416 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.345097.210.0685.9119.2
3.454.3499.910.0613.8219.9
3.013.4510010.0733.58310.1
2.743.0110010.0843.17110.3
2.542.7410010.0912.84810.4
2.392.5410010.0952.54610.4
2.272.3910010.0962.14610.4
2.172.2710010.1012.00110.5
2.092.1710010.1081.70710.5
2.022.0910010.1191.56910.5
1.952.0210010.1341.40310.5
1.91.9510010.1491.21510.5
1.851.910010.1691.08910.5
1.81.8510010.1980.94710.5
1.761.810010.2340.85810.5
1.721.7610010.270.76610.5
1.691.7210010.2950.71410.5
1.661.6910010.340.69910.5
1.631.6610010.3940.64910.4
1.61.6310010.4940.64910.4
ReflectionResolution: 1.6→50 Å / Num. all: 41416 / Num. obs: 41416 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.081 / Χ2: 1.901 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6310.40.49420460.6491100
1.63-1.6610.40.39420370.6491100
1.66-1.6910.50.3420640.6991100
1.69-1.7210.50.29520260.7141100
1.72-1.7610.50.2720400.7661100
1.76-1.810.50.23420290.8581100
1.8-1.8510.50.19820490.9471100
1.85-1.910.50.16920481.0891100
1.9-1.9510.50.14920801.2151100
1.95-2.0210.50.13420321.4031100
2.02-2.0910.50.11920611.5691100
2.09-2.1710.50.10820541.7071100
2.17-2.2710.50.10120562.0011100
2.27-2.3910.40.09620882.1461100
2.39-2.5410.40.09520862.5461100
2.54-2.7410.40.09120682.8481100
2.74-3.0110.30.08421033.1711100
3.01-3.4510.10.07321143.5831100
3.45-4.349.90.06121313.821199.9
4.34-509.20.06822045.911197.2

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0.394 / FOM acentric: 0.449 / FOM centric: 0 / Reflection: 21410 / Reflection acentric: 18776 / Reflection centric: 2634
Phasing MAD setR cullis acentric: 1.5 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.2 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 18776 / Reflection centric: 2634
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
12.5-501.60.50.24639
7.14-12.51.340.50.3258108
5-7.141.660.50.3737202
3.85-51.070.40.31392284
3.13-3.851.160.30.22261381
2.63-3.131.630.20.13340459
2.27-2.631.930.20.14629541
2-2.272.010.106113620
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
121.33790.1280.1280.1624.947
223.2886-0.186-0.0120.2844.985
323.8171-0.0670.1410.2734.825
425.1166-0.110.0130.2174.255
530.0717-0.4640.1710.3373.893
627.5195-0.3040.1830.3483.864
740.58640.160.2160.2223.53
849.7612-0.183-0.110.243.589
954.08890.021-0.0110.342.89
1034.150.06-0.0130.3291.361
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-500.2590.4790854639
7.14-12.50.3270.4640366258108
5-7.140.4210.5370939737202
3.85-50.4410.531016761392284
3.13-3.850.4360.509026422261381
2.63-3.130.4290.488037993340459
2.27-2.630.410.458051704629541
2-2.270.3340.368067336113620
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 45428
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.86-10077.50.372517
5.31-6.86660.842639
4.49-5.3159.90.886778
3.96-4.4958.70.895886
3.58-3.96610.887982
3.3-3.5859.80.8831082
3.07-3.3610.8751146
2.88-3.0763.10.8561226
2.73-2.8862.30.8541291
2.59-2.7363.70.8611383
2.48-2.5961.60.8541433
2.38-2.4862.10.8451508
2.29-2.3863.60.8311524
2.21-2.2962.20.851607
2.13-2.2164.30.8191664
2.07-2.1363.60.8081711
2.01-2.0764.40.8061756
1.95-2.0184.90.8021790
1.9-1.9590.80.7711871
1.86-1.991.10.7891909
1.81-1.8688.30.7771930
1.77-1.8188.10.7452015
1.73-1.7794.30.7292024
1.7-1.7390.80.7512079
1.66-1.790.20.6882119
1.63-1.66890.6972138
1.6-1.63910.6152202
1.55-1.690.30.4824218

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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: 1.6→36.55 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1966 / WRfactor Rwork: 0.161 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9204 / SU B: 2.744 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0911 / SU Rfree: 0.0907 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.091
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
Rfree0.192 2075 5 %RANDOM
Rwork0.1572 ---
all0.159 41229 --
obs0.159 41229 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.94 Å2 / Biso mean: 26.3713 Å2 / Biso min: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 66 386 3147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022959
X-RAY DIFFRACTIONr_bond_other_d0.0020.022002
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9974038
X-RAY DIFFRACTIONr_angle_other_deg1.03234928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74224.234111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41115495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2961518
X-RAY DIFFRACTIONr_chiral_restr0.1810.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213338
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02564
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 126 -
Rwork0.172 2591 -
all-2717 -
obs--96.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4810.2284-0.04230.8909-0.13520.665-0.0127-0.0479-0.0007-0.03190.0066-0.0653-0.00380.08280.00610.07060.0045-0.00030.0520.00820.042824.782449.169219.0807
20.73420.1384-0.01110.608-0.13270.85350.0036-0.1442-0.0340.0923-0.03290.10710.0752-0.06310.02930.0856-0.00040.00520.08420.03550.11161.35440.711433.9579
30.43990.1018-0.03190.8538-0.16030.47150.00850.0344-0.0287-0.14130.03510.10940.05070.0004-0.04350.0914-0.0019-0.0350.04670.01520.058912.698643.755111.2656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 139
2X-RAY DIFFRACTION2A140 - 268
3X-RAY DIFFRACTION3A269 - 385

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