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

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Basic information

Entry
Database: PDB / ID: 4pdh
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM POLAROMONAS SP JS666 (Bpro_1871, TARGET EFI-510164) BOUND TO D-ERYTHRONATE
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsSOLUTE-BINDING 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
(2R,3R)-2,3,4-trihydroxybutanoic acid / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesPolaromonas sp. JS666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 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 / Refinement description / 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 / pdbx_validate_symm_contact / software
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 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification
Revision 2.0Dec 25, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,1662
Polymers33,0301
Non-polymers1361
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.153, 112.539, 148.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 33029.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. JS666 (bacteria) / Gene: Bpro_1871 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12CD8
#2: Chemical ChemComp-EAX / (2R,3R)-2,3,4-trihydroxybutanoic acid / erythronic acid


Mass: 136.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (36.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-ERYTHRONATE); Reservoir (60 %(v/v) tacsimate); Cryoprotection (100% Tascimate pH 7.0)

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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 9, 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: 1.8→89.64 Å / Num. obs: 33226 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.16 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.061 / Net I/σ(I): 9.5 / Num. measured all: 238160 / Scaling rejects: 5
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
1.8-1.847.10.62631409719750.252100
9-89.645.40.10514.416683070.0594.9

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PDD

4pdd


Resolution: 1.8→39.475 Å / FOM work R set: 0.901 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1708 1680 5.06 %
Rwork0.1367 31518 -
obs0.1385 33198 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.31 Å2 / Biso mean: 21.73 Å2 / Biso min: 7.32 Å2
Refinement stepCycle: final / Resolution: 1.8→39.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 9 367 2700
Biso mean--13.6 33.11 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012393
X-RAY DIFFRACTIONf_angle_d1.2553227
X-RAY DIFFRACTIONf_chiral_restr0.073356
X-RAY DIFFRACTIONf_plane_restr0.008423
X-RAY DIFFRACTIONf_dihedral_angle_d14.437902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8530.19741430.17925832726100
1.853-1.91280.21471270.161726142741100
1.9128-1.98110.20091350.148325792714100
1.9811-2.06050.1581360.134725902726100
2.0605-2.15420.16791380.123526062744100
2.1542-2.26780.14621300.123226282758100
2.2678-2.40990.18321420.129825952737100
2.4099-2.59590.18931450.144226072752100
2.5959-2.85710.17081520.144726212773100
2.8571-3.27030.18941260.146226662792100
3.2703-4.11960.13941480.119526662814100
4.1196-39.48420.17241580.13642763292199
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)
10.23680.44370.07392.01830.89060.7098-0.04480.06970.2053-0.16990.078-0.0916-0.22680.0028-0.04410.14790.0153-0.01590.122-0.03530.1833-13.0031-10.2961-23.1868
20.567-0.143-0.1210.79770.28581.1218-0.0286-0.0815-0.02640.16160.0489-0.05670.16170.0174-0.02120.10230.0161-0.00840.1087-0.01510.0966-13.8138-30.9829-19.9826
30.60370.61120.58712.01171.69662.0872-0.0272-0.04370.09230.0284-0.07880.1287-0.1388-0.2210.09580.10980.0337-0.00670.1305-0.03250.1288-22.8257-19.1357-24.4833
40.25840.0456-0.47250.09070.06761.5750.0038-0.0292-0.07690.11490.01370.14750.3944-0.4635-0.0270.2874-0.0610.02890.2363-0.01010.2101-24.8028-41.1723-15.5663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 74 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 259 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 294 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 295 through 335 )A0

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