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

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Basic information

Entry
Database: PDB / ID: 4eyk
TitleCrystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris BisB5 in complex with 3,4-dihydroxy benzoic acid
ComponentsTwin-arginine translocation pathway signal
KeywordsTRANSPORT PROTEIN / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,4-DIHYDROXYBENZOIC ACID / Twin-arginine translocation pathway signal
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsChang, C. / Mack, J. / Zerbs, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins.
Authors: Michalska, K. / Chang, C. / 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 1.1Sep 12, 2012Group: Database references
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Twin-arginine translocation pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1993
Polymers39,9831
Non-polymers2162
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.611, 131.901, 130.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

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Components

#1: Protein Twin-arginine translocation pathway signal


Mass: 39983.023 Da / Num. of mol.: 1 / Fragment: UNP residues 27-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: BisB5 / Gene: RPD_1586 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q13AR6
#2: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M SODIUM CITRATE, 20% ISO-PROPANOL,20% PEG 4000, pH 5.6, 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: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 31877 / Num. obs: 31855 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 38.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 3.27 / Num. unique all: 1595 / % possible all: 100

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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: 1.9→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.987 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.113
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
Rfree0.1824 1611 5.1 %RANDOM
Rwork0.133 ---
all0.1356 31816 --
obs0.1356 31816 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.51 Å2 / Biso mean: 37.0376 Å2 / Biso min: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å20 Å2
2--0.44 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 15 252 2999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022898
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9773927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8235383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32525.263114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55515506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3511511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212198
X-RAY DIFFRACTIONr_rigid_bond_restr2.8832898
X-RAY DIFFRACTIONr_sphericity_free33.691579
X-RAY DIFFRACTIONr_sphericity_bonded23.11253009
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 112 -
Rwork0.173 1981 -
all-2093 -
obs-2093 96.59 %
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)
10.204-0.1263-0.12450.1010.21050.8667-0.02590.0126-0.02550.0418-0.01830.02170.1764-0.08190.04420.0727-0.0270.00980.0363-0.00090.016916.596810.506883.1839
20.10320.0273-0.04410.13530.02330.080.0058-0.00610.00960.0046-0.001-0.0002-0.0079-0.0023-0.00480.0436-0.00160.00060.0336-0.00120.012126.195938.286382.1175
30.00060.0003-0.00120.043-0.03160.0261-0.00570.00320.0008-0.03550.0130.00640.0288-0.0226-0.00730.0535-0.0129-0.00490.05490.00280.010521.35621.355765.0284
40.0505-0.0945-0.03620.18350.03040.3122-0.01190.006-0.00470.0197-0.00690.00810.08190.00880.01880.0651-0.00030.00580.0340.00060.012828.61787.656277.0788
50.0088-0.0051-0.01040.05670.03150.02450.00120.0003-0.0020.0004-0.001-0.00730.0018-0.0035-0.00020.04540.0006-0.00010.03810.00280.014731.926928.553571.3566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 146
2X-RAY DIFFRACTION2A147 - 276
3X-RAY DIFFRACTION3A277 - 304
4X-RAY DIFFRACTION4A305 - 359
5X-RAY DIFFRACTION5A360 - 390

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