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- PDB-6guq: Crystal structure of GanP, a glucose-galactose binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 6guq
TitleCrystal structure of GanP, a glucose-galactose binding protein from Geobacillus stearothermophilus, in complex with glucose
ComponentsPutative sugar binding protein
KeywordsSUGAR BINDING PROTEIN / Glucose-galactose binding protein / Geobacillus stearothermophilus / three-component sensing system / galactan utilization system
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Putative sugar binding protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.385 Å
AuthorsSherf, D. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: The crystal structure of GanP, a glucose-galactose binding protein from Geobacillus stearothermophilus, in complex with glucose
Authors: Sherf, D. / Zehavi, A. / Lansky, S. / Shoham, Y. / Shoham, G.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7032
Polymers35,5221
Non-polymers1801
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint5 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.970, 70.970, 149.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative sugar binding protein


Mass: 35522.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: ganP / Production host: Escherichia coli (E. coli) / References: UniProt: W8QN64
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.5 buffer), and 20% w/v PEG 10K. Crystals were soaked with 30 mM of glucose and 15% PEG 10K solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.38→47.44 Å / Num. obs: 17967 / % possible obs: 99.8 % / Redundancy: 29.81 % / CC1/2: 1 / Rmerge(I) obs: 0.111 / Net I/σ(I): 29.37
Reflection shellResolution: 2.38→2.53 Å / Redundancy: 2.43 % / Rmerge(I) obs: 1.87 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 2831 / CC1/2: 0.944 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C6Q

3c6q


Resolution: 2.385→38.66 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.61
RfactorNum. reflection% reflection
Rfree0.2441 1074 6 %
Rwork0.1977 --
obs0.2006 17906 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.385→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 12 63 2237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082219
X-RAY DIFFRACTIONf_angle_d0.8893011
X-RAY DIFFRACTIONf_dihedral_angle_d4.9731854
X-RAY DIFFRACTIONf_chiral_restr0.055357
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3846-2.49320.35121280.31422021X-RAY DIFFRACTION98
2.4932-2.62460.36081320.28222083X-RAY DIFFRACTION99
2.6246-2.7890.3311320.26062069X-RAY DIFFRACTION100
2.789-3.00420.3111330.24322069X-RAY DIFFRACTION100
3.0042-3.30640.32731330.24192085X-RAY DIFFRACTION100
3.3064-3.78450.24311350.20362111X-RAY DIFFRACTION100
3.7845-4.76670.23131370.16882141X-RAY DIFFRACTION100
4.7667-38.66510.17781440.1572253X-RAY DIFFRACTION100

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