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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 / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP/TeaA / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / TRAP dicarboxylate transporter subunit DctP
Function and homology information
Specimen sourcePseudomonas putida ND6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.4 Å resolution
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. / 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, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 26, 2014 / Release: Jan 28, 2015
RevisionDateData content typeGroupProviderType
1.0Jan 28, 2015Structure modelrepositoryInitial release
1.1Oct 7, 2015Structure modelExperimental preparation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter subunit DctP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3285
Polyers38,7211
Non-polymers6084
Water5,567309
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)990
ΔGint (kcal/M)-16
Surface area (Å2)12520
MethodPISA
Unit cell
γ
α
β
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-MC 1 2 1
Detailsbiological unit is a monomer

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Components

#1: Protein/peptide TRAP dicarboxylate transporter subunit DctP


Mass: 38720.898 Da / Num. of mol.: 1 / Source: (gene. exp.) Pseudomonas putida ND6 (bacteria) / Gene: YSA_07416 / Plasmid name: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I3UZ52
#2: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Formula: C9H19NO3S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Formula: SO4 / Sulfate
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Formula: H2O / Water

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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 / Density percent sol: 34.52 %
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Details: MIRRORS / Detector: CCD / Collection date: Oct 13, 2014
RadiationMonochromator: GRAPHITE / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 10.2 Å2 / D resolution high: 1.4 Å / D resolution low: 59.99 Å / Number obs: 53215 / CC half: 0.995 / Rmerge I obs: 0.123 / Rpim I all: 0.06 / NetI over sigmaI: 9.2 / Number measured all: 266420 / Redundancy: 5 % / Scaling rejects: 1 / Percent possible obs: 99.2
Reflection shell

Diffraction ID: 1 / Rejects: _

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber measured allNumber unique allCC halfRpim I allRedundancyPercent possible all
0.7801.4001.4302.3001387427740.7220.3815.00099.900
0.0887.41059.99016.60010002860.9800.0523.50071.700

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
RefineOverall FOM work R set: 0.903 / Overall SU ML: 0.12 / Cross valid method: THROUGHOUT / Sigma F: 1.34 / Overall phase error: 16.74 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 61.23 Å2 / B iso mean: 12.21 Å2 / B iso min: 2.35 Å2
Least-squares processR factor R free: 0.1862 / R factor R work: 0.1562 / R factor obs: 0.1577 / Highest resolution: 1.4 Å / Lowest resolution: 26.503 Å / Number reflection R free: 2699 / Number reflection R work: 50501 / Number reflection obs: 53200 / Percent reflection R free: 5.07 / Percent reflection obs: 99.07
Refine hist #finalHighest resolution: 1.4 Å / Lowest resolution: 26.503 Å / B iso mean ligand: 14.46 / B iso mean solvent: 23.55 / Number residues total: 306
Number of atoms included #finalProtein: 2377 / Nucleic acid: 0 / Ligand: 56 / Solvent: 309 / Total: 2742
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0102476
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
Refine LS shell

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

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
1.40000.23490.21491.425514926042753100.0000
1.42550.25590.21151.452914226772819100.0000
1.45290.26350.19931.482515226442796100.0000
1.48250.19760.18271.514814026862826100.0000
1.51480.21960.17921.550014626312777100.0000
1.55000.20100.16111.588813226772809100.0000
1.58880.18460.14801.631713826802818100.0000
1.63170.18500.14641.679714426762820100.0000
1.67970.17850.14171.733913626802816100.0000
1.73390.19280.14531.795914626432789100.0000
1.79590.17790.13841.867813626832819100.0000
1.86780.17050.14101.952713626982834100.0000
1.95270.17770.13562.055712426922816100.0000
2.05570.17020.13142.184415126732824100.0000
2.18440.15690.13452.35301552647280299.0000
2.35300.17570.14512.58961372685282299.0000
2.58960.17840.15552.96391522655280798.0000
2.96390.18370.15513.73251462656280297.0000
3.73250.18920.174726.50801372514265190.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.05950.0229-0.05300.0277-0.02970.0461-0.00010.12340.0278-0.01430.00910.0095-0.0281-0.1027-0.00110.04000.0056-0.00950.04610.01310.047335.672426.345224.9431
20.0160-0.0023-0.02020.0402-0.00390.0155-0.1022-0.0012-0.0696-0.01210.0381-0.04320.0738-0.0047-0.02220.0591-0.02120.00600.0613-0.01090.079334.197411.620330.5875
30.16140.0505-0.11670.13980.11110.1383-0.01670.0070-0.00870.02970.0208-0.00710.01360.0625-0.00090.03770.0038-0.00680.0459-0.00850.039446.012418.306741.5835
40.4171-0.0725-0.19360.0787-0.02450.2666-0.1289-0.24680.09060.1954-0.04150.0179-0.01560.0612-0.02920.0771-0.00950.00700.0533-0.00580.084237.85549.534852.4461
50.1879-0.0020-0.00760.1404-0.12240.26100.02990.03040.04650.03150.00900.0366-0.0448-0.01140.00330.0346-0.00140.00880.0218-0.00760.031837.132523.688541.7371
60.04040.0055-0.0103-0.0017-0.02010.0547-0.0093-0.0585-0.01140.0191-0.0517-0.1124-0.01860.16120.00700.0620-0.0040-0.01250.10470.00670.070256.739417.826049.1145
Refine TLS group

Beg auth asym ID: A / Beg auth seq ID: _ / End auth asym ID: A / End auth seq ID: _ / Refine ID: X-RAY DIFFRACTION

IDRefine TLS IDSelection details
11chain 'A' and (resid 25 through 63 )
22chain 'A' and (resid 64 through 80 )
33chain 'A' and (resid 81 through 163 )
44chain 'A' and (resid 164 through 191 )
55chain 'A' and (resid 192 through 294 )
66chain 'A' and (resid 295 through 330 )

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