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

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Entry
Database: PDB / ID: 7bcr
TitleCrystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with galactonate
ComponentsPutative TRAP transporter solute receptor DctP
KeywordsSUGAR BINDING PROTEIN / sugar acid substrate binding protein TRAP transporter
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 / L-galactonic acid / Putative TRAP transporter solute receptor DctP
Function and homology information
Biological speciesAdvenella mimigardefordensis DPN7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 7, 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)37,2132
Polymers37,0171
Non-polymers1961
Water5,242291
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 area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.034, 62.210, 88.647
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-2Q2 / L-galactonic acid


Mass: 196.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: PEG4000 / 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: 2→50.92 Å / Num. obs: 156928 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 27.81 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.49
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.22 / Num. unique obs: 15796

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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: 2→50.92 Å / SU ML: 0.2992 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.4672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 1199 5.33 %
Rwork0.1963 21299 -
obs0.2 22498 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 2→50.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 13 291 2708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182461
X-RAY DIFFRACTIONf_angle_d1.15553322
X-RAY DIFFRACTIONf_chiral_restr0.0607377
X-RAY DIFFRACTIONf_plane_restr0.0074430
X-RAY DIFFRACTIONf_dihedral_angle_d6.3598324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.40611310.25062312X-RAY DIFFRACTION98.75
2.08-2.170.32221250.2432297X-RAY DIFFRACTION98.78
2.17-2.290.3711330.24632313X-RAY DIFFRACTION98.19
2.29-2.430.29491350.21182342X-RAY DIFFRACTION99.48
2.43-2.620.30231230.2162343X-RAY DIFFRACTION98.72
2.62-2.880.29141410.2082362X-RAY DIFFRACTION99.6
2.88-3.30.28391310.19652391X-RAY DIFFRACTION99.41
3.3-4.160.2481350.1762408X-RAY DIFFRACTION99.88
4.16-50.920.19581450.17062531X-RAY DIFFRACTION99.63

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