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- PDB-7bcn: Crystal structure of the sugar acid binding protein DctPAm from A... -

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Basic information

Entry
Database: PDB / ID: 7bcn
TitleCrystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with Xylonic acid
ComponentsPutative TRAP transporter solute receptor DctP
KeywordsTRANSPORT PROTEIN / transport binding protein sugar binding
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / D-xylonic acid / Putative TRAP transporter solute receptor DctP
Function and homology information
Biological speciesAdvenella mimigardefordensis DPN7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchaefer, L. / Meinert, C. / Kobus, S. / Hoeppner, A. / Smits, S.H. / Steinbuechel, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)417919780 Germany
CitationJournal: Febs J. / Year: 2021
Title: Crystal structure of the sugar acid-binding protein CxaP from a TRAP transporter in Advenella mimigardefordensis strain DPN7 T .
Authors: Schafer, L. / Meinert-Berning, C. / Kobus, S. / Hoppner, A. / Smits, S.H.J. / Steinbuchel, A.
History
DepositionDec 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative TRAP transporter solute receptor DctP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1832
Polymers37,0171
Non-polymers1661
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.110, 62.349, 97.645
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Putative TRAP transporter solute receptor DctP / Putative TRAP transporter solute receptor / DctP family


Mass: 37017.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Advenella mimigardefordensis DPN7 (bacteria)
Gene: MIM_c39430 / Production host: Escherichia coli (E. coli) / References: UniProt: R4JTF7
#2: Chemical ChemComp-TK8 / D-xylonic acid / (2~{R},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentanoic acid / (2R,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid / xylonic acid


Mass: 166.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: Peg4000 pH 7.2 / PH range: 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.967 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.7→32.06 Å / Num. obs: 159256 / % possible obs: 96.45 % / Redundancy: 4.1 % / Biso Wilson estimate: 22.23 Å2 / Rmerge(I) obs: 0.05716 / Net I/σ(I): 15.12
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.42 / Num. unique obs: 16753 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BBR

7bbr


Resolution: 1.7→32.06 Å / SU ML: 0.188 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2025 1792 2.47 %
Rwork0.1723 70771 -
obs0.1731 72563 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 11 474 2889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01252469
X-RAY DIFFRACTIONf_angle_d1.24973332
X-RAY DIFFRACTIONf_chiral_restr0.0566379
X-RAY DIFFRACTIONf_plane_restr0.0082431
X-RAY DIFFRACTIONf_dihedral_angle_d6.6366352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.31861610.27495543X-RAY DIFFRACTION97.59
1.75-1.80.29651330.24185501X-RAY DIFFRACTION97.52
1.8-1.860.23611270.21175534X-RAY DIFFRACTION97.5
1.86-1.920.25131470.20435471X-RAY DIFFRACTION97.53
1.92-20.24621170.195582X-RAY DIFFRACTION97.29
2-2.090.19751630.17685469X-RAY DIFFRACTION97.32
2.09-2.20.18931310.16545449X-RAY DIFFRACTION96.37
2.2-2.340.23911250.16475387X-RAY DIFFRACTION95.13
2.34-2.520.18121210.16194641X-RAY DIFFRACTION81.78
2.52-2.770.22261380.16245441X-RAY DIFFRACTION96.47
2.77-3.170.19351340.16395567X-RAY DIFFRACTION98.6
3.17-3.990.17381520.16235584X-RAY DIFFRACTION98.69
3.99-32.060.18571430.16475602X-RAY DIFFRACTION99.07

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