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

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Basic information

Entry
Database: PDB / ID: 4evr
TitleCrystal structure of ABC transporter from R. palustris - solute binding protein (RPA0668) in complex with benzoate
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
BENZOIC ACID / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 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 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: Putative ABC transporter subunit, substrate-binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3642
Polymers39,2421
Non-polymers1221
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.306, 57.778, 133.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 39241.891 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.08 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M sodium acetate, 25% PEG4000, 8% 2-propanol, 5 mM sodium benzoate, pH 8.0, 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 3, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.84→40 Å / Num. all: 29016 / Num. obs: 28325 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 24.75 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2.05 / Num. unique all: 1383 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84→22.62 Å / Cor.coef. Fo:Fc: 0.9545 / Cor.coef. Fo:Fc free: 0.9424 / SU R Cruickshank DPI: 0.187 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Details: hydrogen atoms have been added at riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1428 5.05 %RANDOM
Rwork0.1501 ---
all0.1518 28268 --
obs0.1518 28268 96.57 %-
Displacement parametersBiso mean: 33.23 Å2
Baniso -1Baniso -2Baniso -3
1-5.7266 Å20 Å20 Å2
2--0.026 Å20 Å2
3----5.7525 Å2
Refine analyzeLuzzati coordinate error obs: 0.201 Å
Refinement stepCycle: LAST / Resolution: 1.84→22.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 9 174 2816
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0155380HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.239777HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1485SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes784HARMONIC5
X-RAY DIFFRACTIONt_it5380HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.45
X-RAY DIFFRACTIONt_other_torsion2.83
X-RAY DIFFRACTIONt_chiral_improper_torsion355SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5893SEMIHARMONIC4
LS refinement shellResolution: 1.84→1.91 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2171 121 4.61 %
Rwork0.1766 2506 -
all0.1785 2627 -
obs-2627 96.57 %
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)
11.58510.0868-0.61231.20660.15911.8273-0.12680.0844-0.5144-0.0601-0.0980.05140.41270.00570.22480.0155-0.0060.0551-0.1058-0.01340.012628.892727.18434.5292
20.03322.39691.07092.8756-0.07190-0.0639-0.1583-0.52270.0799-0.12240.09240.2719-0.41660.18630.0234-0.11710.1476-0.11430.01940.105415.821224.295814.3606
32.5479-0.2326-0.46490.45520.00862.3925-0.1377-0.4876-0.54420.2054-0.04210.08820.54420.06950.17990.0317-0.00270.0722-0.08870.1134-0.035127.204426.334219.8909
40.8962-1.1761-0.34311.6664-0.25213.24310.0042-0.54270.30660.2955-0.0242-0.1069-0.33960.29160.02010.0082-0.10710.02550.0824-0.152-0.078630.614754.162328.0121
51.9080.0207-0.75060.7719-0.1691.610.1026-0.54420.32050.2463-0.07240.1666-0.1844-0.0334-0.0302-0.0282-0.04650.06190.0383-0.1149-0.069419.471850.357326.1253
62.08260.1569-0.57170.77570.10981.02380.1123-0.23170.34470.0592-0.07430.0571-0.17260.1261-0.038-0.0239-0.0290.0157-0.0623-0.0338-0.009628.743350.782613.1026
71.9750.1086-0.46560.5175-0.27652.7643-0.0909-0.2051-0.48450.0668-0.0839-0.0050.47280.36540.1748-0.02780.05630.0344-0.08290.0655-0.017538.480328.51411.3153
82.7885-1.13360.34285.4751-2.81972.32120.0606-0.52190.0310.413-0.1629-0.151-0.13750.44140.1023-0.0685-0.0442-0.00160.0382-0.0186-0.13538.017743.955820.4809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|32 - A|79}A32 - 79
2X-RAY DIFFRACTION2{A|80 - A|95}A80 - 95
3X-RAY DIFFRACTION3{A|96 - A|155}A96 - 155
4X-RAY DIFFRACTION4{A|156 - A|174}A156 - 174
5X-RAY DIFFRACTION5{A|175 - A|224}A175 - 224
6X-RAY DIFFRACTION6{A|225 - A|292}A225 - 292
7X-RAY DIFFRACTION7{A|293 - A|358}A293 - 358
8X-RAY DIFFRACTION8{A|359 - A|391}A359 - 391

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