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- PDB-4evq: Crystal structure of ABC transporter from R. palustris - solute b... -

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Basic information

Entry
Database: PDB / ID: 4evq
TitleCrystal structure of ABC transporter from R. palustris - solute binding protein (RPA0668) in complex with 4-hydroxybenzoate
ComponentsPutative ABC transporter subunit, substrate-binding component
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ABC transporter / solute binding protein / benzoate-derivatives binding
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / P-HYDROXYBENZOIC ACID / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsMichalska, K. / Mack, J.C. / Zerbs, S. / Collart, F.R. / 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
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: 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: Putative ABC transporter subunit, substrate-binding component
B: Putative ABC transporter subunit, substrate-binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,66715
Polymers78,4842
Non-polymers1,18313
Water11,548641
1
A: Putative ABC transporter subunit, substrate-binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9779
Polymers39,2421
Non-polymers7368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative ABC transporter subunit, substrate-binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6896
Polymers39,2421
Non-polymers4475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.428, 183.940, 76.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-838-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative ABC transporter subunit, substrate-binding component


Mass: 39241.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: hbaE, RPA0668 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: G3XCQ4

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Non-polymers , 6 types, 654 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Li2SO4, 0.1 M sodium acetate/acetic acid, 30% PEG8K, 5mM sodium 4-hydroxybenzoate, pH 4.5, 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: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 145161 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.8 / Num. unique all: 7121 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
PHENIX(phenix.refine: 1.7.1_742)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→35.15 Å / SU ML: 0.27 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 13.97 / Stereochemistry target values: ML
Details: hydrogen atoms have been added at the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1748 1460 1.01 %thin resolution shells
Rwork0.1392 ---
all0.1395 145034 --
obs0.1395 145034 99.8 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.518 Å2 / ksol: 0.447 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6662 Å20 Å20 Å2
2--2.6017 Å2-0 Å2
3---0.0645 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5351 0 73 641 6065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155741
X-RAY DIFFRACTIONf_angle_d1.6157797
X-RAY DIFFRACTIONf_dihedral_angle_d12.0332072
X-RAY DIFFRACTIONf_chiral_restr0.097860
X-RAY DIFFRACTIONf_plane_restr0.0111027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4006-1.45060.24871460.195514125X-RAY DIFFRACTION99
1.4506-1.50870.20481460.147214207X-RAY DIFFRACTION100
1.5087-1.57740.13791460.118514241X-RAY DIFFRACTION100
1.5774-1.66060.15131460.101214265X-RAY DIFFRACTION100
1.6606-1.76460.13691460.099614268X-RAY DIFFRACTION100
1.7646-1.90080.16031460.104114311X-RAY DIFFRACTION100
1.9008-2.09210.12391460.113314382X-RAY DIFFRACTION100
2.0921-2.39480.15071460.117914417X-RAY DIFFRACTION100
2.3948-3.01690.17041460.148214487X-RAY DIFFRACTION100
3.0169-35.16450.22011460.174814871X-RAY DIFFRACTION99

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