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

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Basic information

Entry
Database: PDB / ID: 4pak
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER EISENIAE EF01-2 (Veis_3954, TARGET EFI-510324) A NEPHRIDIAL SYMBIONT OF THE EARTHWORM EISENIA FOETIDA, BOUND TO (R)-PANTOIC ACID
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 / carbohydrate binding
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
PANTOATE / Solute-binding protein Veis_3954
Similarity search - Component
Biological speciesVerminephrobacter eiseniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 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)
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 1.2Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.3Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9848
Polymers36,2611
Non-polymers7247
Water10,359575
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.023, 78.023, 110.477
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-653-

HOH

21A-672-

HOH

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 36260.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verminephrobacter eiseniae (bacteria) / Strain: EF01-2 / Gene: Veis_3954 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1WPV4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PAF / PANTOATE / 2,4-DIHYDROXY-3,3-DIMETHYL-BUTYRATE


Mass: 147.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (67.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM (R)-Pantoic Acid); Reservoir ( 2.0 M Ammonium Sulfate, 0.1 M Bis-Tris pH 5.5); Cryoprotection (20% Reservoir + 80% 2.0M LiSO4)

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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: 1.2→110.48 Å / Num. obs: 121721 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 8.94 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.033 / Net I/σ(I): 13.5 / Num. measured all: 1204310 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.2-1.228.20.7992.84922459750.294100
6.57-110.4890.04836.875768410.01798.3

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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: 1.2→24.895 Å / FOM work R set: 0.9197 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1642 11813 5.03 %Random Selection
Rwork0.1533 222941 --
obs0.1539 234754 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.34 Å2 / Biso mean: 13.18 Å2 / Biso min: 4.09 Å2
Refinement stepCycle: final / Resolution: 1.2→24.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 51 575 2968
Biso mean--10.57 25.04 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092502
X-RAY DIFFRACTIONf_angle_d1.2413400
X-RAY DIFFRACTIONf_chiral_restr0.071372
X-RAY DIFFRACTIONf_plane_restr0.007451
X-RAY DIFFRACTIONf_dihedral_angle_d12.992926
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 (%)
1.2-1.21360.2564110.25573257736100
1.2136-1.22790.28174310.262474497880100
1.2279-1.24290.26423670.238274357802100
1.2429-1.25860.23624170.227174817898100
1.2586-1.27520.19713790.222474667845100
1.2752-1.29270.24673520.242773917743100
1.2927-1.31110.24313800.229374317811100
1.3111-1.33070.20154050.205874247829100
1.3307-1.35150.19364120.192874667878100
1.3515-1.37360.20293900.184474337823100
1.3736-1.39730.18383910.180174747865100
1.3973-1.42270.18424450.16974087853100
1.4227-1.45010.1624000.160973937793100
1.4501-1.47970.18623940.164874557849100
1.4797-1.51190.1594310.146474057836100
1.5119-1.5470.15993310.143175237854100
1.547-1.58570.16093990.137474207819100
1.5857-1.62860.15274080.131375197927100
1.6286-1.67650.13543540.128774047758100
1.6765-1.73060.14063760.126174997875100
1.7306-1.79240.1523970.126374107807100
1.7924-1.86420.14824000.127374697869100
1.8642-1.9490.1843750.17457438781399
1.949-2.05170.13533610.126974787839100
2.0517-2.18020.14164310.119674487879100
2.1802-2.34840.18733830.167169755297
2.3484-2.58450.13333840.127374597843100
2.5845-2.95790.14613710.137374777848100
2.9579-3.72470.14534310.141174027833100
3.7247-24.90060.14854070.14417390779799
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)
12.6701-0.1708-0.42570.13550.07930.1893-0.0245-0.0051-0.1304-0.03420.02560.24790.0887-0.28280.01790.0742-0.0211-0.010.14520.01790.1296-14.115242.72942.0371
20.6858-0.1118-0.24490.3302-0.00890.62540.01970.00050.0251-0.00380.01170.0173-0.0057-0.0098-0.03240.05220.0039-0.00650.03720.00690.05126.232350.377544.0398
34.5262-1.0487-2.79680.58210.63932.1975-0.0831-0.013-0.22890.03190.00360.07360.1532-0.05520.10020.0669-0.0076-0.01640.05420.01090.0711-1.268436.946945.1846
40.4643-0.3164-0.60520.32580.82482.5549-0.0289-0.0898-0.03290.020.0344-0.01560.12830.1721-0.01260.07220.0126-0.01280.0810.01350.071419.391547.332852.2445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 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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