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- PDB-4ey3: Crystal structure of solute binding protein of ABC transporter in... -

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Basic information

Entry
Database: PDB / ID: 4ey3
TitleCrystal structure of solute binding protein of ABC transporter in complex with p-hydroxybenzoic 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
P-HYDROXYBENZOIC ACID / Twin-arginine translocation pathway signal
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 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
SupersessionMay 30, 2012ID: 3T0N
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 9, 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)40,1212
Polymers39,9831
Non-polymers1381
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.816, 132.625, 130.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
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: 2.2→50 Å / Num. all: 20231 / Num. obs: 19925 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.22 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.541 / Num. unique all: 488 / % possible all: 96.3

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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: 2.22→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.418 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.209
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
Rfree0.2341 1025 5.2 %RANDOM
Rwork0.1816 ---
all0.1842 19857 --
obs0.1842 19857 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.15 Å2 / Biso mean: 50.547 Å2 / Biso min: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å20 Å20 Å2
2---3.76 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.22→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 10 112 2859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.022811
X-RAY DIFFRACTIONr_angle_refined_deg0.9831.9743796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0555365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55725.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94615490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0851511
X-RAY DIFFRACTIONr_chiral_restr0.0680.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212105
X-RAY DIFFRACTIONr_rigid_bond_restr1.51932811
X-RAY DIFFRACTIONr_sphericity_free37.637564
X-RAY DIFFRACTIONr_sphericity_bonded25.95552806
LS refinement shellResolution: 2.223→2.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 50 -
Rwork0.238 978 -
all-1028 -
obs-1028 72.96 %
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)
10.0010.000200.0005-0.00040.00030.00110.00190.00570.0035-0.00190.0012-0.00280.00240.00090.03310.0028-0.00110.1058-0.00040.035416.618710.417883.7217
20.0850.0441-0.10030.0271-0.05160.12020.0112-0.0035-0.00120.0164-0.00650.0046-0.00990.0019-0.00470.03430.00080.00170.0866-0.00480.026526.044238.487482.6649
30.3403-0.01310.43010.1961-0.00010.54590.00270.010.00710.0033-0.01450.04520.00550.01910.01180.02630.0064-0.00450.0772-0.00090.026721.270421.380565.4467
40.0431-0.039-0.07380.25610.10950.201-0.00920.0266-0.01090.0346-0.0079-0.01550.03720.02820.01710.03540.00530.00110.0953-0.00660.026328.70637.738777.6018
50.4549-0.20610.2880.4178-0.35410.3369-0.00480.01660.0120.0209-0.0125-0.0237-0.01880.01390.01730.03410.00340.00170.0886-0.00550.025631.798528.707771.8261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 146
2X-RAY DIFFRACTION2A147 - 276
3X-RAY DIFFRACTION3A277 - 304
4X-RAY DIFFRACTION4A305 - 359
5X-RAY DIFFRACTION5A360 - 390

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