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- PDB-4nn3: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4nn3
TitleCrystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens (Desal_2161), Target EFI-510109, with bound orotic acid
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 / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / 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
OROTIC ACID / TRIETHYLENE GLYCOL / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesDesulfovibrio salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 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
DepositionNov 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,3314
Polymers39,9891
Non-polymers3423
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.346, 147.006, 39.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-692-

HOH

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Components

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


Mass: 39988.789 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_2161 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6BW16
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 1.78 Å3/Da / Density % sol: 30.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40.2 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, reservoir: MCSG1(H9) (0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350), cryoprotection: 4:1 50% w/v PEG3350:reservoir, ligand copurified with ...Details: 40.2 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, reservoir: MCSG1(H9) (0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350), cryoprotection: 4:1 50% w/v PEG3350:reservoir, ligand copurified with protein, 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: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 8, 2013 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→147.006 Å / Num. all: 53494 / Num. obs: 53494 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 10.45 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.484.40.61.33023969140.684.7
1.48-1.574.80.4031.93384169900.40389.5
1.57-1.6750.292.73360467150.2991.8
1.67-1.815.20.2053.73341664420.20593.8
1.81-1.985.40.1295.83321360970.12996.4
1.98-2.215.90.0848.73315956260.08497.8
2.21-2.566.40.063113194850170.06398.7
2.56-3.136.80.05312.12945043210.05399
3.13-4.436.90.03616.82362534280.03699.4
4.43-147.0066.50.02522.11272119440.02597.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
MOSFLMdata reduction
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: STRUCTURE SOLVED INITIALLY IN SAME CRYSTAL FORM SOAKED WITH SODIUM IODIDE AND SAD PHASED

Resolution: 1.4→30.728 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8762 / SU ML: 0.13 / σ(F): 0 / σ(I): 0 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 2726 5.1 %RANDOM
Rwork0.1529 ---
all0.1547 53419 --
obs0.1547 53419 93.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.58 Å2 / Biso mean: 16.6572 Å2 / Biso min: 4.63 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 22 434 2907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092541
X-RAY DIFFRACTIONf_angle_d1.2323427
X-RAY DIFFRACTIONf_chiral_restr0.061367
X-RAY DIFFRACTIONf_plane_restr0.007450
X-RAY DIFFRACTIONf_dihedral_angle_d15.913967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.42550.29751250.26712162228778
1.4255-1.45290.27661320.23762453258586
1.4529-1.48250.27671470.22942466261389
1.4825-1.51480.23841220.21172523264589
1.5148-1.550.24151420.19512541268390
1.55-1.58880.25031440.18172540268490
1.5888-1.63170.22031200.17412603272391
1.6317-1.67970.21961230.17172601272492
1.6797-1.73390.19471640.15632608277293
1.7339-1.79590.21661570.15932677283494
1.7959-1.86780.1841530.14692707286095
1.8678-1.95280.17811440.14432752289697
1.9528-2.05570.17841500.14312786293697
2.0557-2.18450.19441420.1412794293697
2.1845-2.35310.16951540.13472812296698
2.3531-2.58980.15861550.14042854300999
2.5898-2.96430.171460.14612858300499
2.9643-3.73370.17051630.13242918308199
3.7337-30.73580.16471430.14373038318197
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)
10.94330.05540.54290.4598-0.11821.4394-0.0356-0.02830.15780.0454-0.0064-0.1064-0.230.19620.04020.1058-0.0274-0.00820.0811-0.00250.110324.942330.741216.0804
22.8855-0.51250.56481.418-0.53271.93240.01610.2616-0.0368-0.19840.1483-0.1179-0.02840.2161-0.16620.0835-0.02710.01840.15-0.01110.097125.791924.27170.6684
30.74970.17010.14870.59280.18360.59810.007-0.0129-0.07530.02990.0089-0.0320.09830.0379-0.01780.08070.0092-0.00390.06030.01350.089416.719712.476510.8708
40.6568-0.14520.19060.36660.07131.08070.03210.0940.0154-0.042-0.03690.001-0.0675-0.07660.0020.07050.01240.00670.0670.00940.05598.908321.36061.0629
51.07360.06090.50180.32650.17491.16440.0032-0.09080.0270.0198-0.03110.0223-0.0701-0.16170.02760.08910.01150.01330.06530.00690.07988.609925.66515.0407
61.1151-0.45010.55890.326-0.02380.67290.1195-0.0155-0.27080.0984-0.06810.15070.2219-0.085-0.0470.1494-0.0188-0.00910.09690.00590.17437.53963.31747.522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 67 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 84 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 139 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 252 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 296 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 297 through 338 )A0

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