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- PDB-5dvj: Crystal structure of galactose complexed periplasmic glucose bind... -

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Basic information

Entry
Database: PDB / ID: 5dvj
TitleCrystal structure of galactose complexed periplasmic glucose binding protein (ppGBP) from P. putida CSV86
ComponentsBinding protein component of ABC sugar transporter
KeywordsTRANSPORT PROTEIN / Periplasmic glucose binding protein / sugar ABC transporter / galactose bound complex / crystallization / Pseudomonas
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-galactopyranose / Binding protein component of ABC sugar transporter
Function and homology information
Biological speciesPseudomonas putida CSV86 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 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 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)90,9788
Polymers90,2422
Non-polymers7376
Water20,4111133
1
A: Binding protein component of ABC sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5855
Polymers45,1211
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area15310 Å2
MethodPISA
2
B: Binding protein component of ABC sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3933
Polymers45,1211
Non-polymers2722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.650, 118.880, 66.570
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-975-

HOH

21B-1060-

HOH

31B-1115-

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-GAL / beta-D-galactopyranose


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1133 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 76051 / % possible obs: 99.9 % / Redundancy: 10.1 % / Net I/σ(I): 19.97
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10 % / Mean I/σ(I) obs: 3.66 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementResolution: 1.8→19.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.415 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22936 3803 5 %RANDOM
Rwork0.17721 ---
obs0.1798 72247 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.599 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å2-0 Å2
2---0.74 Å2-0 Å2
3----1.57 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6002 0 46 1138 7186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196206
X-RAY DIFFRACTIONr_bond_other_d0.0020.025829
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.9418460
X-RAY DIFFRACTIONr_angle_other_deg0.9313.00113394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0425.889270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50415965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9091515
X-RAY DIFFRACTIONr_chiral_restr0.1180.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021389
X-RAY DIFFRACTIONr_mcbond_it0.6520.7843181
X-RAY DIFFRACTIONr_mcbond_other0.6480.7843180
X-RAY DIFFRACTIONr_mcangle_it1.0461.1733977
X-RAY DIFFRACTIONr_mcangle_other1.0461.1743978
X-RAY DIFFRACTIONr_scbond_it1.0040.8843025
X-RAY DIFFRACTIONr_scbond_other0.990.8783017
X-RAY DIFFRACTIONr_scangle_other1.5461.2774467
X-RAY DIFFRACTIONr_long_range_B_refined6.4339.0058406
X-RAY DIFFRACTIONr_long_range_B_other6.177.2437708
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 274 -
Rwork0.267 5208 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6350.7346-1.25293.2867-2.32162.9079-0.1060.28-0.0645-0.35930.16490.11430.1181-0.4158-0.05890.0682-0.008-0.00880.1553-0.02870.062968.57419.89445.381
20.55650.25650.26191.43520.05312.78660.0512-0.0461-0.07550.1108-0.0318-0.174-0.028-0.0269-0.01940.0127-0.0074-0.01290.0099-0.00480.064479.88214.29860.885
33.8152-0.06411.224510.19723.75083.380.23750.2413-1.00060.98790.0211-0.77550.51750.4187-0.25860.2427-0.0135-0.18140.1216-0.01650.538878.267-9.15465.92
40.64750.1741-0.56040.617-0.18032.67610.0342-0.04510.0308-0.0645-0.0419-0.0192-0.2431-0.18940.00770.04260.0303-0.02350.0325-0.01950.069762.186-15.55742.83
55.0446-3.5372-3.0042.51121.63469.5792-0.3173-0.10120.59350.37240.123-0.4496-3.0211-1.48060.19431.31760.6766-0.29410.5585-0.12140.166553.92-7.49228.062
61.31940.3784-1.22570.8928-0.65133.696-0.03360.1176-0.0689-0.13460.0049-0.0349-0.1139-0.39320.02870.04560.0367-0.00920.0616-0.0210.033461.78-18.59541.963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 84
2X-RAY DIFFRACTION2A85 - 402
3X-RAY DIFFRACTION3A403 - 421
4X-RAY DIFFRACTION4B26 - 238
5X-RAY DIFFRACTION5B239 - 266
6X-RAY DIFFRACTION6B267 - 421

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