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- PDB-4n91: Crystal structure of a trap periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4n91
TitleCrystal structure of a trap periplasmic solute binding protein from anaerococcus prevotii dsm 20548 (Apre_1383), target EFI-510023, with bound alpha/beta d-glucuronate
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
beta-D-glucopyranuronic acid / alpha-D-glucopyranuronic acid / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesAnaerococcus prevoti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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)40,3935
Polymers39,7751
Non-polymers6184
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules

A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,78610
Polymers79,5502
Non-polymers1,2368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3950 Å2
ΔGint-20 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.216, 107.216, 66.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-549-

HOH

31A-603-

HOH

41A-660-

HOH

51A-672-

HOH

61A-768-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 39774.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaerococcus prevoti (bacteria) / Strain: DSM 20548 / Gene: Apre_1383 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7RDZ3

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Sugars , 2 types, 2 molecules

#2: 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
#3: 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

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Non-polymers , 3 types, 280 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (42 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-GLUCURONATE); Reservoir (0.2 M Magnesium Chloride, 0.1 M Citrate pH 5.5, 40% (v/v) PEG400); Cryoprotection (100% Reservoir), sitting ...Details: Protein (42 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-GLUCURONATE); Reservoir (0.2 M Magnesium Chloride, 0.1 M Citrate pH 5.5, 40% (v/v) PEG400); Cryoprotection (100% Reservoir), sitting drop vapor diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX 225 HE / Detector: CCD / Date: Oct 15, 2013 / 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: 1.7→92.852 Å / Num. all: 47522 / Num. obs: 47522 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Biso Wilson estimate: 16.12 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7920.80.759114143067900.75996.9
1.79-1.921.20.521.513692064530.5297.2
1.9-2.0321.70.351213291561180.35197.6
2.03-2.1922.40.227212744256890.22797.8
2.19-2.422.80.1682.912047852750.16898.4
2.4-2.6922.90.1345.111014248030.13498.5
2.69-3.122.80.1085.99736342760.10899.1
3.1-3.822.60.0846.88252836550.08499.2
3.8-5.3822.20.0668.46327728510.06699.4
5.38-28.23120.80.069.43355516120.0698.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→28.231 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.9138 / SU ML: 0.11 / σ(F): 0 / σ(I): 0 / Phase error: 15.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 2407 5.07 %RANDOM
Rwork0.1468 ---
obs0.148 47519 97.72 %-
all-47519 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.99 Å2 / Biso mean: 26.4558 Å2 / Biso min: 7.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 40 278 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112574
X-RAY DIFFRACTIONf_angle_d1.2643493
X-RAY DIFFRACTIONf_chiral_restr0.327376
X-RAY DIFFRACTIONf_plane_restr0.006458
X-RAY DIFFRACTIONf_dihedral_angle_d13.461967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.73480.22251290.18042600272997
1.7348-1.77250.18591280.17152586271496
1.7725-1.81370.1971450.15932598274397
1.8137-1.8590.17651550.1532600275597
1.859-1.90930.21141230.15822616273997
1.9093-1.96550.21411600.1732612277297
1.9655-2.02890.17371320.14172635276797
2.0289-2.10140.16371430.13572651279498
2.1014-2.18550.17031410.12722614275598
2.1855-2.28490.17851460.14062646279298
2.2849-2.40530.14411520.12272646279898
2.4053-2.55590.17651150.12992681279698
2.5559-2.75310.15821610.13892668282999
2.7531-3.02990.15791430.1552667281099
3.0299-3.46760.16141490.15722743289299
3.4676-4.36620.16631420.13462719286199
4.3662-28.23450.17581430.15922830297399
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)
10.077-0.01360.00590.04460.02310.0636-0.00070.0433-0.17930.13630.05840.03310.1206-0.0931-0.00140.13030.0023-0.03920.159-0.0370.20329.253435.429922.0197
20.4832-0.1937-0.20620.31160.19560.51460.15990.1656-0.1753-0.001-0.0404-0.0725-0.0062-0.05050.19620.11540.0791-0.01720.1739-0.03680.132420.469844.397118.4267
30.00410.0088-0.00830.0522-0.03960.03550.0740.2438-0.1882-0.1946-0.0275-0.03110.1843-0.06750.01730.14170.0797-0.00810.2442-0.06410.131921.217443.62458.4366
40.2083-0.1499-0.0860.1308-0.02460.12640.09370.06610.0793-0.0037-0.0171-0.0815-0.1060.03790.03210.13510.03340.02520.1304-0.00380.159725.183162.24228.0121
50.4227-0.1253-0.09170.28460.11310.18410.05610.0996-0.0205-0.0183-0.03580.041-0.0484-0.06470.02410.11280.049100.1256-0.02150.115317.585252.595927.0739
60.42050.14630.06140.4012-0.22570.32880.0370.1464-0.0407-0.0036-0.05050.23910.0618-0.18640.11480.08470.0368-0.03650.1979-0.05370.1626.792945.565918.6034
70.17760.16390.20490.1590.1810.20820.0650.16180.1203-0.07190.0266-0.0118-0.1897-0.0102-0.0010.24390.05350.07420.18280.040.163623.24867.619518.9364
80.5070.31390.14850.48290.1350.05810.05010.2778-0.0351-0.25210.0453-0.0362-0.3715-0.10470.05880.26240.15220.03130.36490.06250.135120.73959.13663.4327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 60 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 125 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 149 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 197 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 255 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 291 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 292 through 317 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 318 through 337 )A0

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