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- PDB-4ze4: Structure of Gan1D, a putative 6-phospho-beta-galactosidase from ... -

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Basic information

Entry
Database: PDB / ID: 4ze4
TitleStructure of Gan1D, a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / TIM-barrel / dimer / glycoside hydrolase / 6-phospho-beta-galactosidase
Function / homology
Function and homology information


6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase activity / carbohydrate catabolic process / beta-glucosidase activity / cytosol
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Putative 6-phospho-beta-galactobiosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.92 Å
AuthorsLansky, S. / Zehavi, A. / Dvir, H. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Structure of Gan1D, a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus
Authors: Lansky, S. / Zehavi, A. / Dvir, H. / Shoham, Y. / Shoham, G.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.title / _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 6-phospho-beta-galactobiosidase
B: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7426
Polymers112,4192
Non-polymers3224
Water9,656536
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-6 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.010, 68.880, 152.880
Angle α, β, γ (deg.)90.00, 100.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-962-

HOH

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Components

#1: Protein Putative 6-phospho-beta-galactobiosidase


Mass: 56209.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: gan1D / Production host: Escherichia coli (E. coli) / References: UniProt: W8QF82, 6-phospho-beta-galactosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.49 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 17% PEG 8K, 3% MPD, 0.1 M imidazole buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.92→40 Å / Num. obs: 86922 / % possible obs: 99.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6
Reflection shellResolution: 1.92→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.92→31.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.433 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24519 4183 5 %RANDOM
Rwork0.1935 ---
obs0.19612 79427 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.825 Å2
Baniso -1Baniso -2Baniso -3
1-3.81 Å20 Å20.96 Å2
2---1.67 Å20 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 1.92→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 22 536 8306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198071
X-RAY DIFFRACTIONr_bond_other_d0.0010.027306
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.92810988
X-RAY DIFFRACTIONr_angle_other_deg0.927316756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1723.547437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.109151250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2311561
X-RAY DIFFRACTIONr_chiral_restr0.1160.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219338
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022079
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6953.2343808
X-RAY DIFFRACTIONr_mcbond_other2.6953.2333807
X-RAY DIFFRACTIONr_mcangle_it3.6924.8394761
X-RAY DIFFRACTIONr_mcangle_other3.6924.8394762
X-RAY DIFFRACTIONr_scbond_it3.0013.4824263
X-RAY DIFFRACTIONr_scbond_other3.0013.4824264
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4685.126219
X-RAY DIFFRACTIONr_long_range_B_refined6.18626.6179999
X-RAY DIFFRACTIONr_long_range_B_other6.18526.61810000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.924→1.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 290 -
Rwork0.324 5669 -
obs--96.91 %

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