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- PDB-4eyo: Crystal structure of solute binding protein of ABC transporter fr... -

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Basic information

Entry
Database: PDB / ID: 4eyo
TitleCrystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris HaA2 in complex with p-coumaric acid
ComponentsExtracellular ligand-binding receptor
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / transporter / lignin degradation product
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 / Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å
AuthorsChang, C. / Mack, J. / 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 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 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 1.5Mar 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 / pdbx_struct_special_symmetry / 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: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3582
Polymers39,1941
Non-polymers1641
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.337, 88.337, 210.284
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

21A-691-

HOH

31A-713-

HOH

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Components

#1: Protein Extracellular ligand-binding receptor


Mass: 39194.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: RPB_3575 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q2IU40
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10 mM Nickel chloride, 0.1M Tris, 20% PEG2000 MME, 10 mM Praseodymium Acetate, pH 8.5, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 55110 / Num. obs: 54612 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 30.4
Reflection shellResolution: 1.7→1.71 Å / Redundancy: 93.5 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.12 / Num. unique all: 1256 / % possible all: 93.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.69→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.08 / SU B: 5.819 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.094
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 2773 5.1 %RANDOM
Rwork0.1705 ---
all0.1733 54540 --
obs0.1733 54540 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.31 Å2 / Biso mean: 29.6055 Å2 / Biso min: 13.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å2-0.7 Å20 Å2
2---1.4 Å20 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 1.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 12 229 2951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022846
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9793871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81824.444108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83115488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3761516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212148
X-RAY DIFFRACTIONr_rigid_bond_restr5.47732846
X-RAY DIFFRACTIONr_sphericity_free35.46583
X-RAY DIFFRACTIONr_sphericity_bonded21.32552933
LS refinement shellResolution: 1.691→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 167 -
Rwork0.295 3247 -
all-3414 -
obs-3414 92.15 %
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)
10.0476-0.0607-0.02770.4794-0.11010.0690.00330.0015-0.0041-0.0380.00950.04280.0104-0.006-0.01280.0074-0.0025-0.00760.00460.0060.011221.231813.67241.2875
20.043-0.05180.03060.0625-0.03690.0218-0.006-0.0088-0.00580.00630.00980.0067-0.0037-0.0058-0.00380.0031-0.0001-0.0020.00650.0110.02191.571233.59765.0356
30.5305-0.67170.46460.8675-0.59140.40750.11940.1470.0189-0.1435-0.14480.00920.09360.1240.02540.02790.0116-0.01810.0820.05690.065417.242129.581-15.6426
40.06310.00760.02360.031-0.02760.0404-0.0090.00710.021-0.011-0.0043-0.00630.00870.00410.01330.0097-0.0013-0.00250.00890.00940.014625.761525.9179-3.0512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 139
2X-RAY DIFFRACTION2A140 - 267
3X-RAY DIFFRACTION3A268 - 302
4X-RAY DIFFRACTION4A303 - 384

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