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- PDB-4mnc: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4mnc
TitleCrystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_4736), Target EFI-510156, with bound benzoyl formate, space group P21
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 / periplasmic space
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
BENZOYL-FORMIC ACID / Solute-binding protein Bpro_4736
Similarity search - Component
Biological speciesPolaromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Scott Glenn, A. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / 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
DepositionSep 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)37,7316
Polymers37,1421
Non-polymers5885
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.197, 58.480, 55.760
Angle α, β, γ (deg.)90.000, 108.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRAP dicarboxylate transporter-DctP subunit / TRAP periplasmic solute binding protein


Mass: 37142.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. (bacteria) / Strain: JS666 / ATCC BAA-500 / Gene: Bpro_4736 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q122C7
#2: Chemical ChemComp-173 / BENZOYL-FORMIC ACID / OXO(PHENYL)ACETIC ACID


Mass: 150.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.01 Å3/Da / Density % sol: 38.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 68.01 mg/mL protein in 10 mM HEPES, pH 7.5, 10 mM benzoyl formate, reservoir: MCSG1(E1) (2.0 M ammonium sulfate, 0.1 M HEPES, pH 7.5), cryoprotection: 4:1 2.0 M lithium sulfate:reservoir, ...Details: 68.01 mg/mL protein in 10 mM HEPES, pH 7.5, 10 mM benzoyl formate, reservoir: MCSG1(E1) (2.0 M ammonium sulfate, 0.1 M HEPES, pH 7.5), cryoprotection: 4:1 2.0 M lithium sulfate:reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Jul 23, 2013 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.05→53.019 Å / Num. all: 130018 / Num. obs: 130018 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 6.04 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.05-1.112.40.3582.233053135870.35868.2
1.11-1.173.20.2263.458816184550.22697.6
1.17-1.253.50.1774.462626177020.177100
1.25-1.363.60.1465.359117165180.146100
1.36-1.483.60.108755060152400.108100
1.48-1.663.60.07110.450159137670.07199.9
1.66-1.923.60.0521344283121440.05299.9
1.92-2.353.60.03915.136835102350.03999.4
2.35-3.323.70.02919.82927079750.02999.9
3.32-58.483.50.02711.41559943950.02798.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.05→33.915 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9438 / SU ML: 0.07 / σ(F): 0 / σ(I): 0 / Phase error: 11.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1444 6531 5.03 %RANDOM
Rwork0.1284 ---
all0.1292 129800 --
obs0.1292 129800 94.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 41.68 Å2 / Biso mean: 9.641 Å2 / Biso min: 2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.05→33.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 37 556 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072650
X-RAY DIFFRACTIONf_angle_d1.2083618
X-RAY DIFFRACTIONf_chiral_restr0.07381
X-RAY DIFFRACTIONf_plane_restr0.007483
X-RAY DIFFRACTIONf_dihedral_angle_d15.429993
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 (%)
1.05-1.06190.25621160.2432428254456
1.0619-1.07440.24491390.23032726286563
1.0744-1.08750.18631770.20043002317970
1.0875-1.10130.19281680.17353378354678
1.1013-1.11580.18462070.17023754396186
1.1158-1.13110.15632080.14824188439697
1.1311-1.14720.14752330.127943344567100
1.1472-1.16440.14672090.120743384547100
1.1644-1.18260.14822600.122242804540100
1.1826-1.20190.13632400.118743354575100
1.2019-1.22270.16272490.138742934542100
1.2227-1.24490.14492140.125743274541100
1.2449-1.26890.13612320.112343454577100
1.2689-1.29480.14532190.127442914510100
1.2948-1.32290.15022160.132643524568100
1.3229-1.35370.13182110.102643214532100
1.3537-1.38750.12222560.103443234579100
1.3875-1.42510.13262370.102143394576100
1.4251-1.4670.12262340.106443454579100
1.467-1.51430.12352470.097842704517100
1.5143-1.56850.10852350.096643194554100
1.5685-1.63130.11492290.095543384567100
1.6313-1.70550.12532230.101343294552100
1.7055-1.79540.1252510.107743374588100
1.7954-1.90790.14532020.12784300450299
1.9079-2.05520.16812400.13524310455099
2.0552-2.2620.1582160.1384270448698
2.262-2.58920.13822240.12784316454099
2.5892-3.26170.14122230.141643944617100
3.2617-33.93260.152160.14264387460398

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