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

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Basic information

Entry
Database: PDB / ID: 4xfe
TitleCrystal structure of a TRAP periplasmic solute binding protein from Pseudomonas putida F1 (Pput_1203), Target EFI-500184, with bound D-glucuronate
ComponentsTRAP dicarboxylate transporter subunit DctP
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
beta-D-glucopyranuronic acid / TRAP dicarboxylate transporter subunit DctP
Similarity search - Component
Biological speciesPseudomonas putida ND6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal structure of a TRAP periplasmic solute binding protein from Pseudomonas putida F1 (Pput_1203), Target EFI-500184, with bound D-glucuronate
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionDec 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Experimental preparation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter subunit DctP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3285
Polymers38,7211
Non-polymers6084
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-16 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.001, 35.054, 60.833
Angle α, β, γ (deg.)90.000, 99.540, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21A-637-

HOH

Detailsbiological unit is a monomer

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Components

#1: Protein TRAP dicarboxylate transporter subunit DctP


Mass: 38720.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida ND6 (bacteria) / Gene: YSA_07416 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I3UZ52
#2: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / D-GLUCURONIC ACID / Glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 1.88 Å3/Da / Density % sol: 34.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (60.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-glucuronate); Reservoir (MCSG2(D3), 0.2M Lithium Sulfate, 0.1 M CAPS pH 10.5, 2.0 M Ammonium Sulfate); Cryoprotection (80% Reservoir, 20% glycerol)

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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: Oct 13, 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: 1.4→59.99 Å / Num. obs: 53215 / % possible obs: 99.2 % / Redundancy: 5 % / Biso Wilson estimate: 10.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.06 / Net I/σ(I): 9.2 / Num. measured all: 266420 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.4-1.4350.782.31387427740.7220.38199.9
7.41-59.993.50.08816.610002860.980.05271.7

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.4→26.503 Å / FOM work R set: 0.903 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1862 2699 5.07 %
Rwork0.1562 50501 -
obs0.1577 53200 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.23 Å2 / Biso mean: 12.21 Å2 / Biso min: 2.35 Å2
Refinement stepCycle: final / Resolution: 1.4→26.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 56 309 2742
Biso mean--14.46 23.55 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012476
X-RAY DIFFRACTIONf_angle_d1.3613350
X-RAY DIFFRACTIONf_chiral_restr0.073373
X-RAY DIFFRACTIONf_plane_restr0.007433
X-RAY DIFFRACTIONf_dihedral_angle_d13.043925
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 (%)
1.4-1.42550.23491490.214926042753100
1.4255-1.45290.25591420.211526772819100
1.4529-1.48250.26351520.199326442796100
1.4825-1.51480.19761400.182726862826100
1.5148-1.550.21961460.179226312777100
1.55-1.58880.2011320.161126772809100
1.5888-1.63170.18461380.14826802818100
1.6317-1.67970.1851440.146426762820100
1.6797-1.73390.17851360.141726802816100
1.7339-1.79590.19281460.145326432789100
1.7959-1.86780.17791360.138426832819100
1.8678-1.95270.17051360.14126982834100
1.9527-2.05570.17771240.135626922816100
2.0557-2.18440.17021510.131426732824100
2.1844-2.3530.15691550.13452647280299
2.353-2.58960.17571370.14512685282299
2.5896-2.96390.17841520.15552655280798
2.9639-3.73250.18371460.15512656280297
3.7325-26.5080.18921370.17472514265190
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)
10.05950.0229-0.0530.0277-0.02970.0461-0.00010.12340.0278-0.01430.00910.0095-0.0281-0.1027-0.00110.040.0056-0.00950.04610.01310.047335.672426.345224.9431
20.016-0.0023-0.02020.0402-0.00390.0155-0.1022-0.0012-0.0696-0.01210.0381-0.04320.0738-0.0047-0.02220.0591-0.02120.0060.0613-0.01090.079334.197411.620330.5875
30.16140.0505-0.11670.13980.11110.1383-0.01670.007-0.00870.02970.0208-0.00710.01360.0625-0.00090.03770.0038-0.00680.0459-0.00850.039446.012418.306741.5835
40.4171-0.0725-0.19360.0787-0.02450.2666-0.1289-0.24680.09060.1954-0.04150.0179-0.01560.0612-0.02920.0771-0.00950.0070.0533-0.00580.084237.85549.534852.4461
50.1879-0.002-0.00760.1404-0.12240.2610.02990.03040.04650.03150.0090.0366-0.0448-0.01140.00330.0346-0.00140.00880.0218-0.00760.031837.132523.688541.7371
60.04040.0055-0.0103-0.0017-0.02010.0547-0.0093-0.0585-0.01140.0191-0.0517-0.1124-0.01860.16120.0070.062-0.004-0.01250.10470.00670.070256.739417.82649.1145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 63 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 80 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 163 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 191 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 294 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 295 through 330 )A0

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