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

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Basic information

Entry
Database: PDB / ID: 4paf
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RUEGERIA POMEROYI DSS-3 (SPO1773, TARGET EFI-510260) WITH BOUND 3,4-DIHYDROXYBENZOATE
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
3,4-DIHYDROXYBENZOIC ACID / MALONATE ION / Solute-binding protein SPO1773
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_validate_close_contact
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 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 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

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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)36,7413
Polymers36,4841
Non-polymers2562
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.589, 62.983, 75.706
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-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
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 3,4-DIHYDROXYBENZOATE); Reservoir (0.1 M Bis-Tris Propane pH 7, 60 %(v/v) tacsimate); 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 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: 1.6→62.98 Å / Num. obs: 38418 / % possible obs: 95.6 % / Redundancy: 7 % / Biso Wilson estimate: 10.94 Å2 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.056 / Net I/σ(I): 11.2 / Num. measured all: 269298 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.6-1.637.10.70531374619490.28399.8
8.76-62.984.80.07722.912352590.03687.1

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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: 1.6→48.238 Å / FOM work R set: 0.9148 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1673 3620 4.99 %RANDOM
Rwork0.1433 68972 --
obs0.1445 72592 95.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.97 Å2 / Biso mean: 13.54 Å2 / Biso min: 3.12 Å2
Refinement stepCycle: final / Resolution: 1.6→48.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 25 339 2689
Biso mean--18 26.57 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122427
X-RAY DIFFRACTIONf_angle_d1.3583302
X-RAY DIFFRACTIONf_chiral_restr0.082371
X-RAY DIFFRACTIONf_plane_restr0.008434
X-RAY DIFFRACTIONf_dihedral_angle_d14.106880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62110.23121520.218727792931100
1.6211-1.64330.22661600.213428092969100
1.6433-1.66680.22321790.204427442923100
1.6668-1.69170.19111270.195127772904100
1.6917-1.71810.22831540.193427732927100
1.7181-1.74630.20421440.187327782922100
1.7463-1.77640.21811540.172127642918100
1.7764-1.80870.20581550.173127832938100
1.8087-1.84350.18891440.161728222966100
1.8435-1.88110.20311100.166427942904100
1.8811-1.9220.19861790.163727582937100
1.922-1.96670.22211310.143728312962100
1.9667-2.01590.15461310.14328112942100
2.0159-2.07040.16811010.14331901200297
2.0704-2.13130.19291130.1312501261493
2.1313-2.20010.15191340.120627822916100
2.2001-2.27880.1761090.12461959206870
2.2788-2.370.15391450.127527752920100
2.37-2.47790.12251460.122327932939100
2.4779-2.60850.16321440.122828092953100
2.6085-2.77190.1516970.13041973207071
2.7719-2.98590.13671610.134628012962100
2.9859-3.28630.17631260.13862765289199
3.2863-3.76170.14771410.12662561270292
3.7617-4.73870.13531390.10932554269392
4.7387-48.26020.13911440.1492575271992
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)
10.9319-0.30520.06472.31630.24750.494-0.04060.1361-0.0557-0.0835-0.0094-0.01360.1785-0.02470.03410.09640.00240.01380.0618-0.01690.05358.956332.6328-1.3945
20.21090.17930.020.4896-0.14510.4335-0.02710.003-0.0261-0.06270.0101-0.03360.0186-0.01610.02250.04870.00210.01280.0465-0.00320.05235.520537.94349.4221
31.85061.2623-0.50031.2663-0.55090.3242-0.0015-0.0438-0.1050.0199-0.0162-0.10260.04670.02660.01370.05690.0016-0.00260.07870.00040.058416.955437.925217.0796
40.47610.2284-0.14711.4688-0.10640.43290.05670.00360.07850.001-0.0632-0.0053-0.08940.01580.00240.05460.00490.00530.0528-0.0030.04819.365555.84658.9175
50.37570.21640.06910.45770.36741.3326-0.05140.07040.0325-0.04580.03670.1286-0.0905-0.0612-0.00130.0531-0.0021-0.00190.0625-0.01190.09752.671457.50468.7039
60.35170.187-0.0790.71820.04690.42570.00310.05460.0418-0.0463-0.00560.0578-0.0391-0.0169-0.00470.03950.01070.0020.06710.00480.0619.310849.01524.6235
70.52730.618-0.29572.6587-0.8570.5426-0.06860.0147-0.1019-0.1828-0.0324-0.31330.12070.02240.07320.0670.01240.02450.07430.00410.083918.315537.97612.4061
80.18390.0365-0.19150.2713-0.48361.71590.0353-0.0090.05490.0552-0.0457-0.0725-0.16410.14320.01930.0991-0.00260.00540.0753-0.00630.080515.845861.342412.8694
90.96650.0495-0.21080.5135-0.04091.26320.0437-0.16640.02440.074-0.006-0.078-0.1510.3299-0.04260.1007-0.0159-0.02160.130.01310.086524.404746.761520.2141
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 202 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 203 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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