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

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Basic information

Entry
Database: PDB / ID: 4eyg
TitleCrystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris BisB5 in complex with vanillic 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
ISOPROPYL ALCOHOL / 4-HYDROXY-3-METHOXYBENZOATE / Twin-arginine translocation pathway signal
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 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 1.3Nov 20, 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
B: Twin-arginine translocation pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5458
Polymers79,9662
Non-polymers5796
Water9,440524
1
A: Twin-arginine translocation pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2724
Polymers39,9831
Non-polymers2893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Twin-arginine translocation pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2724
Polymers39,9831
Non-polymers2893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.871, 130.541, 70.388
Angle α, β, γ (deg.)90.000, 109.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Twin-arginine translocation pathway signal


Mass: 39983.023 Da / Num. of mol.: 2 / 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-VNL / 4-HYDROXY-3-METHOXYBENZOATE / vanillate


Mass: 167.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 51.63 %
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: 1.86→50 Å / Num. all: 66901 / Num. obs: 66219 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.1
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2789 / % possible all: 83.9

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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: 1.86→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.939 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / 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
Rfree0.1913 3349 5.1 %RANDOM
Rwork0.1349 ---
all0.1378 66140 --
obs0.1378 66140 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.32 Å2 / Biso mean: 30.4867 Å2 / Biso min: 14.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20.55 Å2
2---2.61 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5469 0 40 524 6033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025709
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9777724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19525.294221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93315990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3911520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214290
X-RAY DIFFRACTIONr_rigid_bond_restr2.83235709
X-RAY DIFFRACTIONr_sphericity_free27.9725144
X-RAY DIFFRACTIONr_sphericity_bonded16.02955977
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 220 -
Rwork0.208 4081 -
all-4301 -
obs-4301 88.59 %
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)
10.0424-0.08380.00320.2130.02110.07-0.0125-0.0017-0.00330.05240.01250.0244-0.0018-0.002600.0330.0050.01110.00350.00350.0161-6.662534.343655.8557
20.03550.02420.00030.1148-0.01870.00380.00150.00190.003-0.0055-0.0034-0.00260.00130.00060.00190.02210.00090.00340.0018-0.00020.01542.75133.307627.8366
30.0491-0.0028-0.08870.062-0.0240.1741-0.01350.0013-0.00230.02560.01320.02010.0213-0.00730.00030.02730.00020.0070.00290.00040.0199-2.006716.155244.9511
40.0398-0.05650.07250.2564-0.08410.1344-0.0089-0.0023-0.00360.04860.014-0.0068-0.011-0.0032-0.00510.02960.00390.00440.001-0.00140.01735.416228.250258.5359
50.0053-0.01820.00330.0708-0.01250.0023-0.0032-0.002-0.00270.01450.0052-0.0001-0.0033-0.0011-0.0020.02260.00040.00150.0049-0.00120.01778.477922.505637.5809
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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