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

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Basic information

Entry
Database: PDB / ID: 4ngu
TitleCrystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio alaskensis G20 (Dde_1548), Target EFI-510103, with bound D-Ala-D-Ala
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP periplasmic solute binding family / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


cell envelope / transmembrane transport / carbohydrate binding
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
D-ALANINE / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesDesulfovibrio alaskensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / 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
DepositionNov 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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)36,3185
Polymers36,0081
Non-polymers3104
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.607, 91.607, 129.027
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 36008.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio alaskensis (bacteria) / Strain: G20 / Gene: Dde_1548 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q311Q1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHIS ENTRY CONTAINS THE LIGAND D-ALANINE-D-ALANINE.

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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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 36.8 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Ala-D-Ala, reservoir: 0.2 M sodium chloride, 0.1 M acetate, pH 4.5, 1.26 M ammonium sulfate, cryoprotection: 4:1 1.8 M lithium ...Details: 36.8 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Ala-D-Ala, reservoir: 0.2 M sodium chloride, 0.1 M acetate, pH 4.5, 1.26 M ammonium sulfate, cryoprotection: 4:1 1.8 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: Oct 17, 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: 2.5→74.695 Å / Num. all: 19702 / Num. obs: 19702 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.6 % / Biso Wilson estimate: 34.76 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / 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
2.5-2.6416.10.76414550728190.764100
2.64-2.816.20.5921.34276826480.592100
2.8-2.9916.10.4041.94071525270.404100
2.99-3.23160.272.83754023420.27100
3.23-3.5415.80.1923.93431321690.192100
3.54-3.9514.90.1584.72957119840.158100
3.95-4.5615.30.0987.22707017640.098100
4.56-5.59150.0877.92272515110.087100
5.59-7.9114.70.0828.41765912030.082100
7.91-129.02712.80.04913.193817350.04999.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→40.968 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8385 / SU ML: 0.27 / σ(F): 0 / σ(I): 0 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 1000 5.12 %RANDOM
Rwork0.1897 ---
all0.1923 19519 --
obs0.1923 19519 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.81 Å2 / Biso mean: 15.8886 Å2 / Biso min: 6.15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 17 172 2643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092526
X-RAY DIFFRACTIONf_angle_d1.1133418
X-RAY DIFFRACTIONf_chiral_restr0.08373
X-RAY DIFFRACTIONf_plane_restr0.005448
X-RAY DIFFRACTIONf_dihedral_angle_d14.082932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.63180.28211590.211325922751100
2.6318-2.79670.29331510.209325832734100
2.7967-3.01250.25121470.206326202767100
3.0125-3.31560.26281390.207126342773100
3.3156-3.79510.27721290.21752561269096
3.7951-4.78020.21081420.15952673281599
4.7802-40.97340.20091330.171528562989100

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