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- PDB-5im2: Crystal structure of a TRAP solute binding protein from Rhodofera... -

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Basic information

Entry
Database: PDB / ID: 5im2
TitleCrystal structure of a TRAP solute binding protein from Rhodoferax ferrireducens T118 (Rfer_2570, TARGET EFI-510210) in complex with copurified benzoate
ComponentsTwin-arginine translocation pathway signal
KeywordsTRANSPORT PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / Twin-arginine translocation pathway signal
Similarity search - Component
Biological speciesRhodoferax ferrireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal structure of a TRAP solute binding protein from Rhodoferax ferrireducens T118 (Rfer_2570, TARGET EFI-510210) in complex with copurified benzoate
Authors: Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMar 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)42,2622
Polymers42,1391
Non-polymers1221
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.014, 71.864, 78.603
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Twin-arginine translocation pathway signal


Mass: 42139.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodoferax ferrireducens (bacteria) / Strain: ATCC BAA-621 / DSM 15236 / T118 / Gene: Rfer_2570 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q21VB6
#2: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


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


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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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

CrystalMosaicity: 1.22 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM 3,4-Dihydroxybenzoate); Reservoir (MCSG1 D12, 0.2 M Ammonium Chloride pH 6.3, 20 %(w/v) PEG 3350); Cryoprotection (20% diethylen glycol, 80% reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 9, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→28.57 Å / Num. obs: 32423 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.049 / Rrim(I) all: 0.13 / Net I/σ(I): 7.9 / Num. measured all: 224541 / Scaling rejects: 52
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.736.80.7171151416930.8010.2970.7771.8100
9-28.5750.0498531710.9980.0220.05413.264.9

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I7I

5i7i


Resolution: 1.7→28.568 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.91
RfactorNum. reflection% reflection
Rfree0.1992 1643 5.08 %
Rwork0.1573 --
obs0.1594 32360 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.79 Å2 / Biso mean: 30.1593 Å2 / Biso min: 10.34 Å2
Refinement stepCycle: final / Resolution: 1.7→28.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 14 236 2740
Biso mean--15.8 34.51 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092580
X-RAY DIFFRACTIONf_angle_d0.9793500
X-RAY DIFFRACTIONf_chiral_restr0.056383
X-RAY DIFFRACTIONf_plane_restr0.008453
X-RAY DIFFRACTIONf_dihedral_angle_d10.5831548
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.750.24811460.218325042650100
1.75-1.80650.29291340.211225312665100
1.8065-1.87110.28511490.206725292678100
1.8711-1.9460.22161360.199325182654100
1.946-2.03450.1981320.17125442676100
2.0345-2.14170.22331230.171125632686100
2.1417-2.27590.18081360.159825462682100
2.2759-2.45150.17521310.153125762707100
2.4515-2.6980.20431330.159225672700100
2.698-3.08810.22191300.156125862716100
3.0881-3.88910.18121450.142226272772100
3.8891-28.57180.17331480.13322626277496
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)
13.0198-1.108-0.33323.10440.73321.41390.0002-0.0939-0.25640.3836-0.0042-0.10170.21310.05790.01940.2793-0.004-0.09540.15860.02260.1640.1005-8.944575.3759
21.00920.11690.29621.74880.01720.82050.01150.01510.00520.1417-0.0332-0.2460.04980.13750.0270.1203-0.0098-0.04370.1372-0.00250.131538.5662.410166.2381
32.041-0.9070.26033.19140.37751.127-0.1581-0.19120.0120.40090.12030.24660.0954-0.17530.02840.1914-0.00170.02790.167-0.01110.163121.756811.45674.6258
44.4973-0.56220.6631.87020.29331.59390.03470.1992-0.10860.10970.0678-0.59160.27460.3064-0.09790.1610.0253-0.06080.2114-0.02540.23348.6237-8.094964.3922
55.6415-0.9826-4.70432.83470.83577.2229-0.1032-0.1357-0.33380.31580.00670.35220.2692-0.08710.11820.2016-0.05-0.01370.13670.01920.168925.0329-6.168970.2285
63.71071.077-0.85863.5552-0.77621.83320.06120.18840.01130.2923-0.01850.7548-0.3135-0.5778-0.020.16990.00890.01560.2407-0.0720.293711.93589.771667.2514
71.56480.0159-0.00451.59580.05682.2162-0.09750.11810.1646-0.33720.0408-0.0182-0.11390.03420.0530.1987-0.0298-0.04430.17810.02820.131630.66459.124951.9535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 57 )A26 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 153 )A58 - 153
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 239 )A154 - 239
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 266 )A240 - 266
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 290 )A267 - 290
6X-RAY DIFFRACTION6chain 'A' and (resid 291 through 311 )A291 - 311
7X-RAY DIFFRACTION7chain 'A' and (resid 312 through 347 )A312 - 347

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