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- PDB-4pf8: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4pf8
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp. NAS-14.1 (TARGET EFI-510299) WITH BOUND BETA-D-GALACTURONATE
ComponentsTRAP-T family transporter, DctP (Periplasmic binding) 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-galactopyranuronic acid / TRAP-T family transporter, DctP (Periplasmic binding) subunit
Similarity search - Component
Biological speciesSulfitobacter sp. NAS-14.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
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
DepositionApr 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Structure summary
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Oct 7, 2015Group: Experimental preparation
Revision 1.4Oct 14, 2015Group: Non-polymer description
Revision 1.5Sep 13, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP-T family transporter, DctP (Periplasmic binding) subunit
B: TRAP-T family transporter, DctP (Periplasmic binding) subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9056
Polymers73,4452
Non-polymers4594
Water13,799766
1
A: TRAP-T family transporter, DctP (Periplasmic binding) subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9523
Polymers36,7231
Non-polymers2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRAP-T family transporter, DctP (Periplasmic binding) subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9523
Polymers36,7231
Non-polymers2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.979, 58.014, 62.968
Angle α, β, γ (deg.)115.620, 104.690, 94.160
Int Tables number1
Space group name H-MP1
Detailsbiological unit is a monomer

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Components

#1: Protein TRAP-T family transporter, DctP (Periplasmic binding) subunit


Mass: 36722.688 Da / Num. of mol.: 2 / Fragment: UNP residues 30-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfitobacter sp. NAS-14.1 (bacteria) / Gene: NAS141_03681 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3T0C3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid / D-Galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (31.8 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Galacturonate); Reservoir (2.4 M Sodium Malonate pH 7.0); Cryoprotection (80% Reservoir + 20% Diethylene Glycol

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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: Apr 2, 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: 1.5→53.85 Å / Num. obs: 106185 / % possible obs: 94.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.41 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.056 / Net I/σ(I): 10.9 / Num. measured all: 414615
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.5-1.5340.6982.32044951750.40693.6
8.22-53.853.30.09322.815834840.0671.2

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OVQ

4ovq


Resolution: 1.5→27.923 Å / FOM work R set: 0.9075 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 16.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.165 10400 5 %Random Selection
Rwork0.1473 197409 --
obs0.1482 106184 92.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.58 Å2 / Biso mean: 18.16 Å2 / Biso min: 4.75 Å2
Refinement stepCycle: final / Resolution: 1.5→27.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 28 766 5380
Biso mean--7.41 32.77 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114756
X-RAY DIFFRACTIONf_angle_d1.2996447
X-RAY DIFFRACTIONf_chiral_restr0.074706
X-RAY DIFFRACTIONf_plane_restr0.008845
X-RAY DIFFRACTIONf_dihedral_angle_d12.9291757
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51710.284030.26336413681693
1.5171-1.53490.26383760.25316620699692
1.5349-1.55360.23863610.24526505686693
1.5536-1.57330.2663460.23226725707193
1.5733-1.5940.26153010.22166445674693
1.594-1.61580.20643040.20976856716093
1.6158-1.63890.21533440.20516518686293
1.6389-1.66340.2263510.19546683703494
1.6634-1.68930.20883660.1876634700094
1.6893-1.7170.19893670.186678704594
1.717-1.74660.18543240.17076771709594
1.7466-1.77840.21063230.16916623694694
1.7784-1.81260.18773300.16146778710894
1.8126-1.84960.16634050.14996707711295
1.8496-1.88980.17573530.1486631698494
1.8898-1.93370.16673740.14246684705894
1.9337-1.98210.15372880.13446644693294
1.9821-2.03570.15353720.13466710708294
2.0357-2.09560.14583740.1326671704594
2.0956-2.16320.15183580.12816705706394
2.1632-2.24040.15753930.13416703709694
2.2404-2.33010.14883520.12446590694293
2.3301-2.43610.16513490.1246574692393
2.4361-2.56450.163220.13616669699193
2.5645-2.7250.14583460.13926586693293
2.725-2.93520.15243270.13736531685892
2.9352-3.23020.16383670.14276312667989
3.2302-3.69670.15293390.12536318665790
3.6967-4.65390.11852980.1176265656388
4.6539-27.92770.15772870.16065860614782
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)
12.6126-1.024-0.32271.92110.12551.03390.0520.201-0.2882-0.2959-0.0996-0.03210.52950.19910.01830.19410.05330.02380.1195-0.00930.11299.20245.54160.3065
23.0735-0.4167-0.27982.3421-0.71741.0215-0.0993-0.2463-0.04370.25380.0467-0.0286-0.01760.04750.04080.10170.0075-0.00270.10440.02340.06164.991412.015613.0639
31.0433-1.07540.44643.0213-0.15950.5917-0.0632-0.14080.04240.25480.0117-0.1626-0.06750.030.04580.0802-0.015-0.00720.1077-0.00460.09258.530823.9148.5162
41.203-0.24120.771.5341-1.22943.0824-0.08040.10280.08120.0601-0.1455-0.4599-0.1280.41620.19370.0856-0.0277-0.02030.15860.02290.185916.523326.18293.6649
51.2982-0.28730.11080.8981-0.30831.03830.06340.0390.1142-0.0349-0.04880.0095-0.1038-0.02740.00120.0759-0.0242-0.0090.04720.00680.0613-2.942528.53212.1051
61.4439-0.05010.06712.92260.23131.3982-0.0581-0.07260.10680.11840.1123-0.142-0.11430.0125-0.04910.0952-0.0020.00220.0864-0.00750.0837-8.016427.659611.0181
70.8917-0.403-0.05581.0303-0.16010.6921-0.0140.00730.0097-0.0317-0.0033-0.06090.0260.02460.01330.0575-0.0143-0.0020.06420.00960.0417-0.467620.46493.0857
83.4108-1.21050.50491.6972-0.86071.36460.05770.25410.0711-0.1893-0.1775-0.15890.19890.2370.08910.13040.01760.02560.12990.00350.05687.55716.1596-6.718
91.9954-0.11650.24632.38590.08760.8945-0.2439-0.03370.41660.05180.1755-0.4154-0.31780.1790.08140.1652-0.01310.00310.1428-0.02840.21483.691438.28565.7692
102.3764-1.30890.05483.2618-0.34241.4575-0.0496-0.19930.04170.12950.0266-0.33370.20310.44930.02030.10280.0304-0.00930.15340.01620.09673.5219-1.233428.5532
112.4602-0.1569-0.15742.7561-0.36741.38360.02450.16520.0373-0.263-0.0606-0.04510.02480.07120.02250.10240.00780.02340.09180.00830.077-3.22393.238916.0681
122.3615-0.56010.28050.69330.21620.5049-0.00030.1663-0.0695-0.09420.00280.01280.0272-0.03570.00930.1055-0.01030.00220.08020.00730.0853-14.6791-1.247820.6255
132.9361-0.466-3.27651.14470.55585.1074-0.185-0.0706-0.41830.0661-0.09740.05420.35670.01520.24790.1407-0.02020.00380.09840.00640.1449-17.1485-9.694725.4327
140.57420.059-0.13980.53180.05050.9708-0.0449-0.080.0650.07620.05410.0696-0.0202-0.10660.00120.0729-0.01290.01350.0827-0.00370.0826-20.01549.582527.1288
153.6503-1.08250.44393.61250.04651.150.05380.0288-0.2875-0.0378-0.03720.28490.0541-0.1423-0.00890.0898-0.0095-0.01140.12110.02350.1167-23.669612.597617.9694
161.0067-0.441-0.07250.5683-0.05590.8177-0.0148-0.01670.06410.02980.0132-0.0435-0.05210.00010.0020.0718-0.0134-0.00480.0577-0.00720.0662-12.835610.857124.5665
171.8903-1.1634-0.30862.48350.32242.0988-0.1957-0.2181-0.10930.34520.10130.10620.23740.06460.08730.12940.0056-0.00540.11320.02210.0525-7.2028-0.554535.5663
182.01450.61491.15832.6381.82463.39090.1972-0.191-0.03910.1121-0.19540.14050.1163-0.5083-0.00350.10860.00160.00420.13250.02090.1139-30.04578.053924.7076
191.5242-0.18741.03951.9284-0.18616.13620.1285-0.0866-0.46990.0079-0.20220.05730.381-0.52120.03490.1755-0.0506-0.05440.1869-0.00520.2557-27.918-8.541818.4779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 63 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 80 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 111 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 134 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 162 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 199 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 200 through 248 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 249 through 283 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 284 through 325 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 25 through 63 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 64 through 80 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 81 through 111 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 112 through 134 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 135 through 162 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 163 through 182 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 183 through 248 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 249 through 283 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 284 through 311 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 312 through 325 )B0

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