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- PDB-4dqd: The crystal structure of a transporter in complex with 3-phenylpy... -

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Basic information

Entry
Database: PDB / ID: 4dqd
TitleThe crystal structure of a transporter in complex with 3-phenylpyruvic acid
ComponentsExtracellular ligand-binding receptor
KeywordsSIGNALING PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural ge nomics / MCSG / Midwest Center for Structural Genomics
Function / homology
Function and homology information


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-HYDROXYPYRUVIC ACID / 3-PHENYLPYRUVIC ACID / Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsTan, K. / 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
DepositionFeb 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7837
Polymers38,9421
Non-polymers8416
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.038, 62.422, 60.623
Angle α, β, γ (deg.)90.00, 113.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

DetailsExperimentally unknown. It is predicted to be monomeric.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Extracellular ligand-binding receptor


Mass: 38942.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: RPB_4630 / References: UniProt: Q2IR47

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Non-polymers , 5 types, 346 molecules

#2: Chemical ChemComp-PPY / 3-PHENYLPYRUVIC ACID / Phenylpyruvic acid


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-3PY / 3-HYDROXYPYRUVIC ACID / Hydroxypyruvic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Trimethylamine N-oxide, 0.1M Tris:HCl, 20% (w/v) PEG MME 2000, pH 8.5, 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: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.6→26 Å / Num. all: 56211 / Num. obs: 56211 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 23
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2210 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3SG0

3sg0


Resolution: 1.601→25.97 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 15.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1623 2848 5.07 %random
Rwork0.1429 ---
all0.1439 56150 --
obs0.1439 56150 99.62 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.379 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7619 Å20 Å20.1312 Å2
2--6.1791 Å20 Å2
3----3.4172 Å2
Refinement stepCycle: LAST / Resolution: 1.601→25.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 57 340 3097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062867
X-RAY DIFFRACTIONf_angle_d1.0993877
X-RAY DIFFRACTIONf_dihedral_angle_d14.2891100
X-RAY DIFFRACTIONf_chiral_restr0.075431
X-RAY DIFFRACTIONf_plane_restr0.005506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6009-1.62850.24131350.21072535X-RAY DIFFRACTION96
1.6285-1.65810.21161490.18432661X-RAY DIFFRACTION100
1.6581-1.690.18721340.17522673X-RAY DIFFRACTION100
1.69-1.72440.18131520.16222616X-RAY DIFFRACTION100
1.7244-1.76190.20581540.15362671X-RAY DIFFRACTION100
1.7619-1.80290.17381470.14772626X-RAY DIFFRACTION100
1.8029-1.8480.19191090.14182717X-RAY DIFFRACTION100
1.848-1.89790.17371410.13862647X-RAY DIFFRACTION100
1.8979-1.95380.16221540.13262687X-RAY DIFFRACTION100
1.9538-2.01680.16551320.12792645X-RAY DIFFRACTION100
2.0168-2.08890.15231370.13092654X-RAY DIFFRACTION100
2.0889-2.17240.15661340.12942704X-RAY DIFFRACTION100
2.1724-2.27130.14581450.12912643X-RAY DIFFRACTION100
2.2713-2.39090.1581440.13552699X-RAY DIFFRACTION100
2.3909-2.54060.15611440.13762646X-RAY DIFFRACTION100
2.5406-2.73660.16161470.14752691X-RAY DIFFRACTION100
2.7366-3.01160.17461420.14482678X-RAY DIFFRACTION100
3.0116-3.44650.15061530.14262681X-RAY DIFFRACTION100
3.4465-4.3390.15191460.13142720X-RAY DIFFRACTION100
4.339-25.97360.1561490.15532708X-RAY DIFFRACTION99
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)
11.90630.57840.04061.08030.06860.93310.0935-0.28020.1310.1149-0.06250.0864-0.1171-0.0602-0.03860.15930.00010.00520.1581-0.02150.15376.81276.264933.6179
21.22380.4341-0.30121.0681-0.2970.71040.0399-0.1846-0.05520.1307-0.0419-0.06630.07380.0746-0.00020.15940.0088-0.01650.140.01070.144811.0924-6.199531.2579
31.48320.1147-0.11550.91360.05021.1592-0.07230.1999-0.1636-0.10570.0889-0.10170.1020.1741-0.02060.16150.00520.01810.1969-0.0350.161126.646-3.33359.3676
41.78670.00020.08260.54320.0170.8639-0.10560.33750.2848-0.11210.1051-0.009-0.15470.0269-0.00480.1879-0.0305-0.01080.18270.03120.160516.81197.67157.465
50.91810.4064-0.0830.8339-0.14081.1990.0089-0.02340.02390.00620.03960.13950.0485-0.1811-0.04850.13180.0085-0.00160.1443-00.1652-0.8442-2.910924.4469
63.0580.4289-0.25263.8241-0.50722.5975-0.17630.60220.0096-0.4290.13730.11560.2472-0.05310.02820.1985-0.0293-0.02830.2422-0.00130.13499.19050.74213.9578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 23:83)
2X-RAY DIFFRACTION2chain 'A' and (resseq 84:139)
3X-RAY DIFFRACTION3chain 'A' and (resseq 140:220)
4X-RAY DIFFRACTION4chain 'A' and (resseq 221:279)
5X-RAY DIFFRACTION5chain 'A' and (resseq 280:365)
6X-RAY DIFFRACTION6chain 'A' and (resseq 366:383)

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