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

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Basic information

Entry
Database: PDB / ID: 4pai
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RUEGERIA POMEROYI DSS-3 (SPO1773, TARGET EFI-510260) WITH BOUND 3-HYDROXYBENZOATE
ComponentsTRAP dicarboxylate transporter, DctP subunit, putative
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


C4-dicarboxylate transport / transmembrane transport / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
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
3-HYDROXYBENZOIC ACID / Solute-binding protein SPO1773
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 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 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter, DctP subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6222
Polymers36,4841
Non-polymers1381
Water7,116395
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.780, 63.020, 75.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit, putative


Mass: 36484.359 Da / Num. of mol.: 1 / Mutation: P37S, Y220C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Strain: DSS-3 / Gene: SPO1773 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LSJ5
#2: Chemical ChemComp-3HB / 3-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (67.94 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM 3-DIHYDROXYBENZOATE); Reservoir (0.1 M Bis-Tris Propane pH 7, 60 %(v/v) tacsimate); 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: Apr 4, 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→21.34 Å / Num. obs: 59822 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.055 / Net I/σ(I): 9.6 / Num. measured all: 399138 / Scaling rejects: 55
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.4-1.426.50.7722.71893629140.327100
7.67-21.345.40.08419.619783680.03886.1

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.4→21.338 Å / FOM work R set: 0.9129 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1654 5786 5.07 %Random Selection
Rwork0.1451 108378 --
obs0.1461 114164 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.6 Å2 / Biso mean: 13.35 Å2 / Biso min: 1.71 Å2
Refinement stepCycle: final / Resolution: 1.4→21.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 15 395 2735
Biso mean--6.08 27.45 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122448
X-RAY DIFFRACTIONf_angle_d1.3543335
X-RAY DIFFRACTIONf_chiral_restr0.083375
X-RAY DIFFRACTIONf_plane_restr0.008439
X-RAY DIFFRACTIONf_dihedral_angle_d13.783890
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 (%)
1.4-1.41590.32562020.275435743776100
1.4159-1.43260.27731610.256736603821100
1.4326-1.450.24832020.240436213823100
1.45-1.46840.22911850.241636023787100
1.4684-1.48770.25482020.237436023804100
1.4877-1.50810.24051850.223336303815100
1.5081-1.52960.24772020.20835953797100
1.5296-1.55240.21751880.194836163804100
1.5524-1.57670.1932210.180936323853100
1.5767-1.60250.17791700.181136283798100
1.6025-1.63010.20032040.17235543758100
1.6301-1.65980.20432130.173736203833100
1.6598-1.69170.15792030.158736333836100
1.6917-1.72620.20142230.154135763799100
1.7262-1.76370.18452170.150735603777100
1.7637-1.80470.16241780.143836663844100
1.8047-1.84980.17721640.138936583822100
1.8498-1.89980.15751740.139336293803100
1.8998-1.95570.15371940.132835993793100
1.9557-2.01880.15481750.129136463821100
2.0188-2.09090.16721580.125836523810100
2.0909-2.17450.13321960.119135993795100
2.1745-2.27340.14382020.115336233825100
2.2734-2.39310.1441980.11736073805100
2.3931-2.54280.12941630.123736563819100
2.5428-2.73870.15921780.123836163794100
2.7387-3.01370.15891800.129836293809100
3.0137-3.44820.15182410.129435803821100
3.4482-4.33830.12581960.107636043800100
4.3383-21.34010.13412110.14063511372298
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)
10.013-0.0112-0.00270.0342-0.00240.0394-0.03580.0244-0.0085-0.04960.0268-0.01630.0555-0.024100.07330.00290.0130.0441-0.01120.05798.992932.688-1.3942
20.06980.0675-0.02950.1125-0.12840.205-0.0167-0.0068-0.0155-0.025-0.0019-0.01890.0169-0.0199-0.01750.02090.00020.01030.0187-0.00450.025.522237.95289.3985
30.02990.01510.01670.00920.00750.00930.0129-0.0032-0.03250.0109-0.0166-0.0311-0.00510.0100.0533-0.0033-0.00060.06990.00960.055517.010637.922217.0911
40.07210.0094-0.10220.03290.01480.16480.036-0.00980.01210.0233-0.0334-0.021-0.03830.0097-0.00010.04550.00130.00620.0425-0.00140.05059.364856.02988.7159
50.03920.02620.00210.0468-0.00740.0057-0.02150.01980.00320.01760.04720.0462-0.02540.0241-00.0455-0.00150.00290.0491-0.010.06192.960457.3279.1827
60.08110.0126-0.07970.10010.0890.181-0.00680.02120.0023-0.02280.00370.025-0.0156-0.0176-00.03390.0041-0.00170.04470.00610.04529.02149.69824.3197
70.1112-0.0633-0.05370.03740.02090.0652-0.03660.0338-0.0491-0.1071-0.0146-0.12440.07060.0115-0.00030.05620.00740.02020.05260.01130.075418.350837.99942.386
80.1127-0.09560.00170.0803-0.00250.03530.01160.00450.01740.0307-0.0327-0.0501-0.0760.0313-0.00050.0876-0.01140.00630.0580.00180.041415.851461.331912.8364
90.05090.0005-0.01070.0852-0.05120.03350.0416-0.0378-0.00430.0576-0.0273-0.0355-0.1230.1010.0120.0704-0.0245-0.01040.10120.01620.052823.684846.87520.5364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 55 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 113 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 137 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 174 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 201 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 250 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 251 through 284 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 285 through 309 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 310 through 334 )A0

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