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

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Basic information

Entry
Database: PDB / ID: 4mhf
TitleCrystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_3107), target EFI-510173, with bound alpha/beta D-Glucuronate, space group P21
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


carbohydrate transport / 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 / alpha-D-glucopyranuronic acid / Solute-binding protein Bpro_3107
Similarity search - Component
Biological speciesPolaromonas (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.46 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Washington, E. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / 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
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
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, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1113
Polymers36,7221
Non-polymers3882
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.480, 45.960, 63.980
Angle α, β, γ (deg.)90.00, 97.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 36722.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas (bacteria) / Strain: JS666 / ATCC BAA-500 / Gene: Bpro_3107 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q128M1
#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: Sugar ChemComp-GCU / alpha-D-glucopyranuronic acid / Glucuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 1.8 Å3/Da / Density % sol: 31.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (> 50 mg/ml, 10 mM Hepes, pH 7.5, 10 mM Glucuronate, 5 mM DTT); Reservoir (2.0 M Ammonium Sulfate, 0.1 M Tris, pH 8.5(MCSG1 F10)); Cryoprotection (20% Diethylene Glycol, 80% of ...Details: Protein (> 50 mg/ml, 10 mM Hepes, pH 7.5, 10 mM Glucuronate, 5 mM DTT); Reservoir (2.0 M Ammonium Sulfate, 0.1 M Tris, pH 8.5(MCSG1 F10)); Cryoprotection (20% Diethylene Glycol, 80% of Reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 23, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.46→63.409 Å / Num. all: 41662 / Num. obs: 41662 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 8.31 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 26.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.46-1.546.30.1334.93616857180.13387.8
1.54-1.646.30.1026.23469955200.10289
1.64-1.756.30.0767.83343252780.07690.7
1.75-1.896.30.05910.33156149720.05991.9
1.89-2.076.40.04712.82966946690.04793.4
2.07-2.326.40.04413.32724042890.04494.7
2.32-2.676.30.04213.82425338350.04296
2.67-3.286.30.03515.92081233090.03597.3
3.28-4.636.20.039151625726090.03998.4
4.63-22.985.90.03914.5869414630.03998.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.46→21.582 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9374 / SU ML: 0.09 / σ(F): 0 / σ(I): 0 / Phase error: 12.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1447 2108 5.06 %RANDOM
Rwork0.1173 ---
obs0.1187 41631 92.18 %-
all-41631 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.73 Å2 / Biso mean: 12.2561 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 1.46→21.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 26 471 2807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082416
X-RAY DIFFRACTIONf_angle_d1.2493266
X-RAY DIFFRACTIONf_chiral_restr0.074371
X-RAY DIFFRACTIONf_plane_restr0.008419
X-RAY DIFFRACTIONf_dihedral_angle_d12.029920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.49910.16041280.13832440256887
1.4991-1.53650.18291170.12432514263188
1.5365-1.57810.1431370.11542539267688
1.5781-1.62450.14431380.11312494263289
1.6245-1.67690.14181260.11492558268490
1.6769-1.73680.16311490.11522543269291
1.7368-1.80630.14931390.11612607274691
1.8063-1.88850.14981460.11362625277192
1.8885-1.9880.13831450.11212620276593
1.988-2.11240.14511560.10612648280493
2.1124-2.27540.13251390.10522716285594
2.2754-2.50410.13881390.10862728286795
2.5041-2.86570.14381550.11672765292096
2.8657-3.60770.14981640.12142794295897
3.6077-21.58390.13551300.13362932306298
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)
10.2712-0.0288-0.15480.172-0.09060.15780.00440.01490.0167-0.0313-0.03560.05420.011-0.077-0.00080.0413-0.01150.00440.0572-0.00740.04416.688519.954246.0672
20.2227-0.05680.19940.14780.06060.24310.031-0.0177-0.05960.014-0.016-0.02560.0263-0.00380.00060.0342-0.00740.00090.03530.00630.043822.939716.355649.5991
30.0966-0.0256-0.00840.18-0.19010.2063-0.03430.00450.05620.081-0.0277-0.0419-0.11420.0332-0.00310.0601-0.011-0.01060.0345-0.00230.03827.001735.363154.3022
40.04520.03330.04280.0491-0.0390.1160.02580.0791-0.01660.0114-0.08890.0094-0.07510.0551-0.00240.0579-0.0043-0.00110.03370.00650.049826.882634.865745.7745
50.2768-0.03730.09220.06330.07990.2222-0.02740.0084-0.0463-0.0679-0.01240.00170.0563-0.0208-0.00720.0429-0.01480.00420.0283-0.00540.034914.070616.465242.2632
60.0415-0.00330.06020.04410.02010.0485-0.02940.14440.1484-0.0913-0.1358-0.18450.00370.1758-0.07020.0654-0.00540.01310.10580.03590.129438.152233.304645.307
70.09460.03790.0490.02060.04120.11170.08120.0468-0.08110.06310.0288-0.06330.1260.05290.00090.0658-0.002-0.02030.06810.00450.093936.022312.775753.9085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 31:86 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 87:158 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 159:221 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 222:240 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 241:289 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 290:305 )A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 306:331 )A0

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