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

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Entry
Database: PDB / ID: 4xeq
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (Deval_0042, TARGET EFI-510114) BOUND TO COPURIFIED (R)-PANTOIC ACID
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
PANTOATE / TRAP dicarboxylate transporter, DctP subunit / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (Deval_0042, TARGET EFI-510114) BOUND TO COPURIFIED (R)-PANTOIC ACID
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionDec 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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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
B: TRAP dicarboxylate transporter, DctP subunit
C: TRAP dicarboxylate transporter, DctP subunit
D: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,8678
Polymers149,2794
Non-polymers5894
Water12,791710
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4672
Polymers37,3201
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4672
Polymers37,3201
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4672
Polymers37,3201
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4672
Polymers37,3201
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.750, 73.600, 100.210
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a monomer

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Components

#1: Protein
TRAP dicarboxylate transporter, DctP subunit


Mass: 37319.715 Da / Num. of mol.: 4 / Fragment: UNP residues 37-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: RCH1 / Gene: Deval_0042 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3ILJ0, UniProt: A0A0E0SY65*PLUS
#2: Chemical
ChemComp-PAF / PANTOATE / 2,4-DIHYDROXY-3,3-DIMETHYL-BUTYRATE


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


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (35.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (0.2 M di-Ammonium Citrate pH 5.0 , 20 %(w/v) PEG 3350); 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: Nov 12, 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
Reflection twinOperator: h,-k,-l / Fraction: 0.4
ReflectionResolution: 1.7→25.26 Å / Num. obs: 131847 / % possible obs: 98.6 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.044 / Net I/σ(I): 12.2 / Num. measured all: 945105 / Scaling rejects: 109
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.7-1.736.90.7082.74398363970.7650.28797.6
9.31-25.266.80.07227.151417540.9960.02988.6

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→25.254 Å / FOM work R set: 0.7488 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.95 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1847 6750 5.12 %
Rwork0.1572 125132 -
obs0.164 131825 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.09 Å2 / Biso mean: 18.84 Å2 / Biso min: 9.21 Å2
Refinement stepCycle: final / Resolution: 1.7→25.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9535 0 40 710 10285
Biso mean--13.28 19.89 -
Num. residues----1211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129778
X-RAY DIFFRACTIONf_angle_d1.37513292
X-RAY DIFFRACTIONf_chiral_restr0.0711508
X-RAY DIFFRACTIONf_plane_restr0.0061733
X-RAY DIFFRACTIONf_dihedral_angle_d15.3663618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.72940.26123450.23646112645792
1.7294-1.76080.24223260.22926189651593
1.7608-1.79470.22763370.22136180651792
1.7947-1.83130.24333490.21376146649593
1.8313-1.87110.22273410.20746165650693
1.8711-1.91460.21173320.20326188652093
1.9146-1.96250.21843580.19616181653993
1.9625-2.01550.2183070.19336244655194
2.0155-2.07480.21513110.19076268657994
2.0748-2.14170.20793280.18846275660394
2.1417-2.21820.19853350.17826207654294
2.2182-2.30690.19153290.17776265659494
2.3069-2.41180.19453030.17056284658794
2.4118-2.53880.21283430.16736350669394
2.5388-2.69760.18913710.16756218658994
2.6976-2.90560.18273160.15816318663494
2.9056-3.19730.1773390.14776375671494
3.1973-3.65830.17323240.13656332665694
3.6583-4.60290.14883150.11356416673195
4.6029-22.92070.16313460.13886419676593

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