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- PDB-6gq0: Crystal structure of GanP, a glucose-galactose binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 6gq0
TitleCrystal structure of GanP, a glucose-galactose binding protein from Geobacillus stearothermophilus
ComponentsPutative sugar binding protein
KeywordsSUGAR BINDING PROTEIN / Glucose-galactose binding protein / Gebacillus stearothermophilus / three-component sensing system / galactan utilization system.
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / carbohydrate binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative sugar binding protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 Gebacillus Stearothermophilus
Authors: Sherf, D. / Zehavi, A. / Lansky, S. / Shoham, Y. / Shoham, G.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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


Theoretical massNumber of molelcules
Total (without water)35,5221
Polymers35,5221
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.719, 67.719, 152.173
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-574-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.5 buffer), and 20% w/v PEG 10K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.94→38.36 Å / Num. obs: 30682 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.128 / Net I/σ(I): 8
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2021 / CC1/2: 0.939 / % possible all: 99.6

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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: 1.94→38.365 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.84
RfactorNum. reflection% reflection
Rfree0.2279 1518 4.98 %
Rwork0.1969 --
obs0.1985 30490 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→38.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 0 198 2378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082239
X-RAY DIFFRACTIONf_angle_d0.9323039
X-RAY DIFFRACTIONf_dihedral_angle_d18.8821372
X-RAY DIFFRACTIONf_chiral_restr0.059357
X-RAY DIFFRACTIONf_plane_restr0.005390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9401-2.00270.33021290.32812540X-RAY DIFFRACTION98
2.0027-2.07430.34071360.27912564X-RAY DIFFRACTION99
2.0743-2.15730.30911340.24542603X-RAY DIFFRACTION99
2.1573-2.25550.27921400.22032615X-RAY DIFFRACTION99
2.2555-2.37440.25771360.21172572X-RAY DIFFRACTION99
2.3744-2.52310.25671370.21622633X-RAY DIFFRACTION99
2.5231-2.71790.26571370.212619X-RAY DIFFRACTION100
2.7179-2.99130.2541350.20712644X-RAY DIFFRACTION100
2.9913-3.42390.22341420.19522654X-RAY DIFFRACTION100
3.4239-4.31290.19281420.17352691X-RAY DIFFRACTION100
4.3129-38.37240.18421500.16812837X-RAY DIFFRACTION100

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