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Basic information

Entry
Database: PDB / ID: 5dvi
TitleHigh resolution crystal Structure of glucose complexed periplasmic glucose binding protein (ppGBP) from P. putida CSV86
ComponentsBinding protein component of ABC sugar transporter
KeywordsTRANSPORT PROTEIN / Periplasmic glucose binding protein / ppGBP / Crystallization / sugar transport / sugar binding pocket / sugar ABC transporter
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / beta-D-glucopyranose / Carbohydrate ABC transporter substrate-binding protein
Function and homology information
Biological speciesPseudomonas putida CSV86 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPandey, S. / Modak, A. / Phale, P.S. / Bhaumik, P.
Funding support India, 2items
OrganizationGrant numberCountry
Dept. of Biotechnology, Govt. of IndiaBT/PR4954/BRB/10/1063/2012 India
Ramalingaswami Fellowship, Dept. of Biotechnology, Govt. of India India
CitationJournal: J.Biol.Chem. / Year: 2016
Title: High Resolution Structures of Periplasmic Glucose-binding Protein of Pseudomonas putida CSV86 Reveal Structural Basis of Its Substrate Specificity
Authors: Pandey, S. / Modak, A. / Phale, P.S. / Bhaumik, P.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Binding protein component of ABC sugar transporter
B: Binding protein component of ABC sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,62715
Polymers90,2422
Non-polymers1,38513
Water17,637979
1
A: Binding protein component of ABC sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6776
Polymers45,1211
Non-polymers5565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-10 kcal/mol
Surface area15010 Å2
MethodPISA
2
B: Binding protein component of ABC sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9509
Polymers45,1211
Non-polymers8298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.940, 119.050, 66.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-612-

HOH

21B-975-

HOH

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Components

#1: Protein Binding protein component of ABC sugar transporter / Periplasmic glucose binding protein / ppGBP


Mass: 45120.875 Da / Num. of mol.: 2 / Fragment: UNP residues 24-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida CSV86 (bacteria) / Strain: CSV86 / Gene: CSV86_10737 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H7BRJ8
#2: Sugar ChemComp-BGC / beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 979 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.79 % / Description: Big rectangular crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1 M phosphate citrate buffer, 2 M ammonium sulphate
PH range: 4.2-4.8 / Temp details: 295

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.25→44.39 Å / Num. obs: 224933 / % possible obs: 99.7 % / Redundancy: 6.24 % / Net I/σ(I): 16.41
Reflection shellResolution: 1.25→1.35 Å / Redundancy: 5.47 % / Mean I/σ(I) obs: 2.71 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→40.76 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.367 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15153 11245 5 %RANDOM
Rwork0.1219 ---
obs0.12339 213608 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.264 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-0 Å2
2---0.89 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.25→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 87 981 7020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026546
X-RAY DIFFRACTIONr_bond_other_d0.0020.026123
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9458994
X-RAY DIFFRACTIONr_angle_other_deg0.871314111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25525.674282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.744151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1641516
X-RAY DIFFRACTIONr_chiral_restr0.1010.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021493
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7372.0653315
X-RAY DIFFRACTIONr_mcbond_other2.7212.0633314
X-RAY DIFFRACTIONr_mcangle_it3.223.1094183
X-RAY DIFFRACTIONr_mcangle_other3.2223.114184
X-RAY DIFFRACTIONr_scbond_it3.6032.2723231
X-RAY DIFFRACTIONr_scbond_other3.5852.2663219
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2283.2984759
X-RAY DIFFRACTIONr_long_range_B_refined5.46419.0598568
X-RAY DIFFRACTIONr_long_range_B_other4.75717.6348006
X-RAY DIFFRACTIONr_rigid_bond_restr3.184312668
X-RAY DIFFRACTIONr_sphericity_free35.3525260
X-RAY DIFFRACTIONr_sphericity_bonded17.349513203
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 811 -
Rwork0.24 15401 -
obs--98.16 %

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