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- PDB-6gt9: Crystal structure of GanP, a glucose-galactose binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 6gt9
TitleCrystal structure of GanP, a glucose-galactose binding protein from Geobacillus stearothermophilus, in complex with galactose
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


cell envelope / 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-galactopyranose / Putative sugar binding protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.894 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 galactose
Authors: Sherf, D. / Zehavi, A. / Lansky, S. / Shoham, Y. / Shoham, G.
History
DepositionJun 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 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

Downloads & links

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Assembly

Deposited unit
A: Putative sugar binding protein
B: Putative sugar binding protein
C: Putative sugar binding protein
D: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,19512
Polymers142,0904
Non-polymers1,1058
Water13,944774
1
A: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7993
Polymers35,5221
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7993
Polymers35,5221
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7993
Polymers35,5221
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7993
Polymers35,5221
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.520, 88.890, 88.880
Angle α, β, γ (deg.)90.00, 95.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative sugar binding protein


Mass: 35522.449 Da / Num. of mol.: 4
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-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M sodium acetate (pH 4 buffer), 26%-28% w/v PEG MME 2K, 0.2 M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→88.89 Å / Num. obs: 87725 / % possible obs: 99.6 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Net I/σ(I): 12
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4369 / CC1/2: 0.866 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C6Q

3c6q


Resolution: 1.894→58.217 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.72
RfactorNum. reflection% reflection
Rfree0.2391 1999 2.28 %
Rwork0.1916 --
obs0.1926 87582 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.894→58.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8812 0 68 774 9654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079098
X-RAY DIFFRACTIONf_angle_d0.88112359
X-RAY DIFFRACTIONf_dihedral_angle_d16.975571
X-RAY DIFFRACTIONf_chiral_restr0.0551467
X-RAY DIFFRACTIONf_plane_restr0.0051575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.894-1.94140.40261390.32325976X-RAY DIFFRACTION98
1.9414-1.99390.31811420.28216078X-RAY DIFFRACTION100
1.9939-2.05250.33131430.25836104X-RAY DIFFRACTION100
2.0525-2.11880.25231440.23386123X-RAY DIFFRACTION100
2.1188-2.19450.26461420.21756111X-RAY DIFFRACTION100
2.1945-2.28240.29031430.20736105X-RAY DIFFRACTION100
2.2824-2.38630.29141420.19916087X-RAY DIFFRACTION100
2.3863-2.51210.25061420.19326121X-RAY DIFFRACTION100
2.5121-2.66950.24081440.19546141X-RAY DIFFRACTION100
2.6695-2.87560.2421430.19866133X-RAY DIFFRACTION100
2.8756-3.16490.25131440.19266134X-RAY DIFFRACTION100
3.1649-3.62280.23691430.17876135X-RAY DIFFRACTION100
3.6228-4.56410.20151430.14976151X-RAY DIFFRACTION99
4.5641-58.2450.15471450.15036184X-RAY DIFFRACTION98

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