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- PDB-4n6k: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4n6k
TitleCrystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens DSM2638, Target EFI-510113 (Desal_0342), complex with diglycerolphosphate
ComponentsTRAP dicarboxylate transporter-DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP periplasmic solute binding family / 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
bis[(2S)-2,3-dihydroxypropyl] hydrogen phosphate / TRAP dicarboxylate transporter-DctP subunit
Similarity search - Component
Biological speciesDesulfovibrio salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4032
Polymers39,1571
Non-polymers2461
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.024, 54.182, 73.508
Angle α, β, γ (deg.)90.000, 104.980, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

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Components

#1: Protein TRAP dicarboxylate transporter-DctP subunit / TRAP periplasmic solute binding protein


Mass: 39156.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio salexigens (bacteria) / Strain: ATCC 14822 / DSM 2638 / NCIB 8403 / VKM B-1763 / Gene: Desal_0342 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6BWG5
#2: Chemical ChemComp-X3X / bis[(2S)-2,3-dihydroxypropyl] hydrogen phosphate / diglycerolphosphate


Mass: 246.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 55.8 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, reservoir: 0.17 M ammonium acetate, 0.085 M sodium acetate, pH 4.6, 25.5% w/v PEG4000, 15% v/v glycerol, cryoprotection: reservoir + 10% ...Details: 55.8 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, reservoir: 0.17 M ammonium acetate, 0.085 M sodium acetate, pH 4.6, 25.5% w/v PEG4000, 15% v/v glycerol, cryoprotection: reservoir + 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.971 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 9, 2013 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 1.2→71.01 Å / Num. all: 95981 / Num. obs: 95981 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 10.93 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.9 / Num. unique all: 13407 / Rsym value: 0.553 / % possible all: 93.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOCALLY COLLECTED DERIVATIVE

Resolution: 1.2→22.313 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.9098 / SU ML: 0.12 / σ(F): 0 / σ(I): 0 / Phase error: 15.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1619 4814 5.02 %RANDOM
Rwork0.1384 ---
all0.1397 95979 --
obs0.1397 95979 97.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.13 Å2 / Biso mean: 19.2715 Å2 / Biso min: 7.33 Å2
Refinement stepCycle: LAST / Resolution: 1.2→22.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 15 403 2855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072581
X-RAY DIFFRACTIONf_angle_d1.1663503
X-RAY DIFFRACTIONf_chiral_restr0.073387
X-RAY DIFFRACTIONf_plane_restr0.008453
X-RAY DIFFRACTIONf_dihedral_angle_d14.096981
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21360.31981570.26442712286988
1.2136-1.22790.29081560.2462899305594
1.2279-1.24290.23591660.22742941310795
1.2429-1.25860.25361400.22312994313496
1.2586-1.27520.24071800.20682990317097
1.2752-1.29260.22761510.2032988313997
1.2926-1.31110.23721610.19172999316096
1.3111-1.33070.22771470.18642991313897
1.3307-1.35150.22671500.17813030318097
1.3515-1.37360.19251470.16553037318497
1.3736-1.39730.19051360.15833038317498
1.3973-1.42270.17991520.15093066321898
1.4227-1.45010.17991630.14223063322698
1.4501-1.47970.16521560.13713010316698
1.4797-1.51180.14591710.1243081325299
1.5118-1.5470.17121540.11833087324198
1.547-1.58570.12371680.11473047321599
1.5857-1.62850.13961800.10863064324499
1.6285-1.67640.13591670.103930793246100
1.6764-1.73050.13751460.109231353281100
1.7305-1.79230.14281630.107631123275100
1.7923-1.86410.12921700.111431103280100
1.8641-1.94890.13961750.115330843259100
1.9489-2.05150.1461700.12331343304100
2.0515-2.180.13961590.120731433302100
2.18-2.34810.14881490.123631503299100
2.3481-2.58410.1371540.127131513305100
2.5841-2.95730.14751790.135331313310100
2.9573-3.72310.14561760.13783102327899
3.7231-22.31640.18511710.15532797296887

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