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

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Basic information

Entry
Database: PDB / ID: 4zen
TitleStructure of Gan1D, a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-beta-galactose
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
6-O-phosphono-beta-D-galactopyranose / IMIDAZOLE / Putative 6-phospho-beta-galactobiosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 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, in complex with 6-phospho-beta-galactose
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 1.1Jul 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 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 6-phospho-beta-galactobiosidase
B: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,32120
Polymers112,4192
Non-polymers1,90218
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-5 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.517, 68.674, 153.281
Angle α, β, γ (deg.)90.00, 99.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-899-

HOH

21A-908-

HOH

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Components

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


Mass: 56209.715 Da / Num. of mol.: 2 / Fragment: UNP residues 2-478
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: Sugar ChemComp-BGP / 6-O-phosphono-beta-D-galactopyranose / BETA-GALACTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-galactose / 6-O-phosphono-D-galactose / 6-O-phosphono-galactose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Galp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-IMD / IMIDAZOLE


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


Mass: 18.015 Da / Num. of mol.: 486 / 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: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 16-18% PEG 8K, 0.1 M imidazole pH 6.5, 3% MPD

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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: Jan 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 83233 / % possible obs: 97.1 % / Redundancy: 3 % / Rsym value: 0.078 / Net I/σ(I): 16.5
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.1 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZEH

4zeh
PDB Unreleased entry


Resolution: 1.93→26.22 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.184 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20187 3831 5 %RANDOM
Rwork0.15676 ---
obs0.15903 72157 91.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.974 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å21.03 Å2
2---1.47 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: 1 / Resolution: 1.93→26.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 124 486 8358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198121
X-RAY DIFFRACTIONr_bond_other_d0.0030.027346
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.93711033
X-RAY DIFFRACTIONr_angle_other_deg0.923316839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73423.641434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44151235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0541558
X-RAY DIFFRACTIONr_chiral_restr0.1210.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022075
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_it3.3243.6223796
X-RAY DIFFRACTIONr_mcbond_other3.3223.6213795
X-RAY DIFFRACTIONr_mcangle_it4.1725.4184743
X-RAY DIFFRACTIONr_mcangle_other4.1725.4184744
X-RAY DIFFRACTIONr_scbond_it4.2294.0224325
X-RAY DIFFRACTIONr_scbond_other4.2284.0234326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9755.8776288
X-RAY DIFFRACTIONr_long_range_B_refined7.50830.3819814
X-RAY DIFFRACTIONr_long_range_B_other7.50830.3859815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.929→1.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 161 -
Rwork0.232 2944 -
obs--51 %

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