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

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Basic information

Entry
Database: PDB / ID: 7bbr
TitleCrystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T
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 / 2-KETO-3-DEOXYGLUCONATE / Putative TRAP transporter solute receptor DctP
Function and homology information
Biological speciesAdvenella mimigardefordensis DPN7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 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 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Advisory / Data collection / Database references
Category: citation / database_2 ...citation / database_2 / diffrn / pdbx_unobs_or_zero_occ_atoms
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 / _diffrn.ambient_temp
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)37,1952
Polymers37,0171
Non-polymers1781
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, we performed size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-2 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.759, 61.850, 88.254
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-KDG / 2-KETO-3-DEOXYGLUCONATE


Mass: 178.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 44.17 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.002 M zinc sulfate heptahydrate, 0.08 M HEPES pH 7.2 and 25 % Jeffamine ED 2003
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 X 16M / 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: 1.3→49.48 Å / Num. obs: 110532 / % possible obs: 97.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 14.21 Å2 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.054 / Net I/σ(I): 13.7
Reflection shellResolution: 1.3→1.34 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10257 / Rrim(I) all: 0.32

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→49.48 Å / SU ML: 0.1177 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 14.4682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1628 4032 5.05 %
Rwork0.1333 75735 -
obs0.1348 79767 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.65 Å2
Refinement stepCycle: LAST / Resolution: 1.3→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 12 562 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752478
X-RAY DIFFRACTIONf_angle_d1.01343347
X-RAY DIFFRACTIONf_chiral_restr0.075377
X-RAY DIFFRACTIONf_plane_restr0.0083436
X-RAY DIFFRACTIONf_dihedral_angle_d5.7678335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.24991580.18962502X-RAY DIFFRACTION96.73
1.32-1.330.20061500.17512503X-RAY DIFFRACTION96.61
1.33-1.350.21441430.17552541X-RAY DIFFRACTION97
1.35-1.370.21051310.16992549X-RAY DIFFRACTION97.45
1.37-1.380.18861190.15372584X-RAY DIFFRACTION97.16
1.38-1.40.19261350.14852545X-RAY DIFFRACTION97.88
1.4-1.430.19831260.13952552X-RAY DIFFRACTION96.99
1.43-1.450.16341280.13572583X-RAY DIFFRACTION97.55
1.45-1.470.161260.13052571X-RAY DIFFRACTION97.97
1.47-1.50.15381510.1262564X-RAY DIFFRACTION97.42
1.5-1.520.17171280.12952603X-RAY DIFFRACTION98.56
1.52-1.550.15151290.12562585X-RAY DIFFRACTION98.55
1.55-1.590.18261600.12592598X-RAY DIFFRACTION98.25
1.59-1.620.15921260.12392586X-RAY DIFFRACTION98.26
1.62-1.660.15691410.12422599X-RAY DIFFRACTION98.67
1.66-1.70.17721720.12632556X-RAY DIFFRACTION98.95
1.7-1.740.17931370.1272603X-RAY DIFFRACTION98.81
1.74-1.80.1717960.12642678X-RAY DIFFRACTION99
1.8-1.850.14631560.11672595X-RAY DIFFRACTION98.85
1.85-1.920.14781540.12122613X-RAY DIFFRACTION99.07
1.92-20.14071360.11692643X-RAY DIFFRACTION98.93
2-2.090.14281420.11672641X-RAY DIFFRACTION99.5
2.09-2.20.16051690.11692629X-RAY DIFFRACTION99.43
2.2-2.340.15211210.11772653X-RAY DIFFRACTION98.89
2.34-2.520.14991220.12342683X-RAY DIFFRACTION99.47
2.52-2.770.16941390.1282694X-RAY DIFFRACTION99.75
2.77-3.170.16421450.13672709X-RAY DIFFRACTION99.83
3.17-3.990.16011280.13862736X-RAY DIFFRACTION99.58
3.99-49.480.1621640.1582837X-RAY DIFFRACTION99.34

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