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- PDB-4p1e: Crystal structure of a trap periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4p1e
TitleCrystal structure of a trap periplasmic solute binding protein from escherichia fergusonii (efer_1530), target EFI-510119, apo open structure, phased with iodide
ComponentsTRAP dicarboxylate transporter, DctP 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
IODIDE ION / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesEscherichia fergusonii (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. ...Vetting, M.W. / Al Obaidi, N.F. / 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
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Structure summary
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
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 / software / struct_keywords
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 / _software.classification / _struct_keywords.text
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,38838
Polymers37,6931
Non-polymers4,69537
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.820, 67.820, 156.351
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-424-

IOD

21A-523-

HOH

31A-551-

HOH

Detailsbiological unit is a monomer

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 37692.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia fergusonii (bacteria) / Strain: ATCC 35469 / DSM 13698 / CDC 0568-73 / Gene: dctP, EFER_1530 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B7LRA7
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.75 Å3/Da / Density % sol: 55.33 % / Description: Hexagonal Bipyramid, 0.15 mM on a side
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (34.8 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (60 %(v/v) Tacsimate pH 7.0); Soak (Three minutes in 1 M NaI + Reservoir); Cryoprotection (20% glycerol + Reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 20, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→58.734 Å / Num. all: 32768 / Num. obs: 32768 / % possible obs: 97.3 % / Redundancy: 12.6 % / Biso Wilson estimate: 15.8 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.176 / Rsym value: 0.145 / Net I/av σ(I): 4.949 / Net I/σ(I): 14 / Num. measured all: 412915
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-26.90.5771.32750540080.2490.5772.883.6
2-2.1210.60.5041.54756145040.1660.5044.498.6
2.12-2.2713.90.4221.86018343200.1190.4226.599.7
2.27-2.45140.3242.45572339870.0920.3248.399.9
2.45-2.69140.243.25231337290.070.2411100
2.69-314.10.1584.64753033770.0480.15815.9100
3-3.4714.10.0927.64243630200.030.09224.6100
3.47-4.25140.05312.33639525930.020.05334.8100
4.25-6.0113.80.058102784720190.0250.05834.3100
6.01-46.95812.70.03118.41542212110.0250.03131.699.8

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.983 Å / FOM work R set: 0.8623 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 1652 5.05 %
Rwork0.1962 31070 -
obs0.1984 32722 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.25 Å2 / Biso mean: 17.01 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 1.9→38.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 37 219 2495
Biso mean--29.46 22.26 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132283
X-RAY DIFFRACTIONf_angle_d1.3583102
X-RAY DIFFRACTIONf_chiral_restr0.074362
X-RAY DIFFRACTIONf_plane_restr0.007399
X-RAY DIFFRACTIONf_dihedral_angle_d13.854826
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 (%)
1.9-1.9560.331160.31672049216579
1.956-2.01910.34251180.27842358247691
2.0191-2.09120.26851280.23112597272598
2.0912-2.1750.25851220.20482643276599
2.175-2.27390.22961370.190326212758100
2.2739-2.39380.23231320.179826322764100
2.3938-2.54380.2291480.174526232771100
2.5438-2.74010.22981580.187226482806100
2.7401-3.01580.25171590.192726242783100
3.0158-3.45190.21131480.183826992847100
3.4519-4.34820.22241430.153527172860100
4.3482-38.99080.21951430.212628593002100
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)
10.24240.0565-0.13280.7156-0.27380.25280.05690.1115-0.0271-0.2808-0.0625-0.07510.02250.03040.00230.11320.02560.03570.14330.00750.116768.316856.5922165.7037
20.46820.17720.12390.26470.14310.56280.058-0.0364-0.06240.0013-0.05710.01110.0504-0.03-0.00240.07410.0215-0.01380.09650.01260.097252.038347.4777170.0951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 105 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 324 )A0

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