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- PDB-9fli: The structure of GanA, the extracellular galactanase of G.protein... -

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Basic information

Entry
Database: PDB / ID: 9fli
TitleThe structure of GanA, the extracellular galactanase of G.proteiniphilus T-6
ComponentsArabinogalactan endo-beta-1,4-galactanase
KeywordsHYDROLASE / GanA / galactanase / Geobacillus proteiniphilus T-6 / Geobacillus stearothermophilus
Function / homology
Function and homology information


arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / pectin catabolic process
Similarity search - Function
Glycosyl hydrolase family 53 / Glycosyl hydrolase family 53 / Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Arabinogalactan endo-beta-1,4-galactanase
Similarity search - Component
Biological speciesGeobacillus proteiniphilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHadad, N. / Lavid, N. / Shulami, S. / Dessau, M. / Shoham, Y. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of GanA, the extracellular galactanase of G.proteiniphilus T-6
Authors: Hadad, N. / Lavid, N. / Shulami, S. / Dessau, M. / Shoham, Y. / Shoham, G.
History
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arabinogalactan endo-beta-1,4-galactanase
B: Arabinogalactan endo-beta-1,4-galactanase
C: Arabinogalactan endo-beta-1,4-galactanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,2606
Polymers270,1403
Non-polymers1203
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-11 kcal/mol
Surface area44100 Å2
Unit cell
Length a, b, c (Å)160.339, 160.339, 155.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Arabinogalactan endo-beta-1,4-galactanase


Mass: 90046.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus proteiniphilus (bacteria) / Gene: ganA / Production host: Escherichia coli (E. coli)
References: UniProt: F8TRX1, arabinogalactan endo-beta-1,4-galactanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.85 Å3/Da / Density % sol: 33.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 35% PEG 2K and 0.1M Sodium citrate at pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→70.04 Å / Num. obs: 32203 / % possible obs: 95.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 33.83 Å2 / CC1/2: 0.92 / Rmerge(I) obs: 0.43 / Rpim(I) all: 0.16 / Rrim(I) all: 0.46 / Net I/σ(I): 3.7
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4495 / CC1/2: 0.7 / Rpim(I) all: 0.37 / Rrim(I) all: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→70.04 Å / SU ML: 0.4139 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.289 1650 4.86 %
Rwork0.2531 32308 -
obs0.2548 32203 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.75 Å2
Refinement stepCycle: LAST / Resolution: 3.2→70.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9030 0 3 36 9069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01129273
X-RAY DIFFRACTIONf_angle_d1.270712582
X-RAY DIFFRACTIONf_chiral_restr0.06761326
X-RAY DIFFRACTIONf_plane_restr0.00861623
X-RAY DIFFRACTIONf_dihedral_angle_d6.02041239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.290.31851320.26632638X-RAY DIFFRACTION99.89
3.29-3.40.3122980.27172704X-RAY DIFFRACTION99.86
3.4-3.520.32031540.27412611X-RAY DIFFRACTION99.86
3.52-3.660.35981110.30472691X-RAY DIFFRACTION99.61
3.66-3.830.38681610.31542603X-RAY DIFFRACTION99.17
3.83-4.030.34171150.2722677X-RAY DIFFRACTION99.39
4.03-4.280.29191500.22922661X-RAY DIFFRACTION99.68
4.28-4.610.22061460.21762674X-RAY DIFFRACTION99.68
4.62-5.080.24031540.21212682X-RAY DIFFRACTION99.75
5.08-5.810.25051200.23262733X-RAY DIFFRACTION99.83
5.81-7.320.25381580.23712742X-RAY DIFFRACTION99.86
7.32-70.040.2671510.24082892X-RAY DIFFRACTION99.51

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