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- PDB-4oif: 3D structure of Gan42B, a GH42 beta-galactosidase from G. -

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Basic information

Entry
Database: PDB / ID: 4oif
Title3D structure of Gan42B, a GH42 beta-galactosidase from G.
ComponentsBeta-galactosidase
KeywordsHYDROLASE / beta-galactosidase. Gan42B / beta-galactosidase / GH42 / Gan42B / homo-trimer / hydolase / Carbohydrate/Sugar Binding / intracellular
Function / homology
Function and homology information


galactose metabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / metal ion binding
Similarity search - Function
Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II ...Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / using phases from it's GanBE323A mutant / Resolution: 2.448 Å
AuthorsSolomon, H.V. / Tabachnikov, O. / Feinberg, H. / Shoham, Y. / Shoham, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization and preliminary crystallographic analysis of GanB, a GH42 intracellular beta-galactosidase from Geobacillus stearothermophilus.
Authors: Solomon, H.V. / Tabachnikov, O. / Feinberg, H. / Govada, L. / Chayen, N.E. / Shoham, Y. / Shoham, G.
History
DepositionJan 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,79431
Polymers240,2953
Non-polymers2,49928
Water27,0951504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-52 kcal/mol
Surface area66930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.840, 181.350, 196.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-galactosidase / Beta-gal


Mass: 80098.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: T-6 / Gene: gan42B, ganB / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: F8TRX0, beta-galactosidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1504 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16-18% PEG 3350, 250 mM NaCl and 100 mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 4, 2010 / Details: mirror
RadiationMonochromator: Diamond crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.448→48.86 Å / Num. all: 95492 / Num. obs: 91957 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.113 / Rsym value: 0.419 / Net I/σ(I): 11.7
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.419 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
REFMACrefinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: using phases from it's GanBE323A mutant
Starting model: PDB ENTRY 4OJW

4ojw
PDB Unreleased entry


Resolution: 2.448→48.859 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU ML: 0.26 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 17.44 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2045 4594 5 %
Rwork0.1329 --
obs0.1365 91872 96.23 %
all-91878 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.15 Å2
Refine analyzeLuzzati sigma a obs: 0.2369 Å
Refinement stepCycle: LAST / Resolution: 2.448→48.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16922 0 153 1504 18579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817843
X-RAY DIFFRACTIONf_angle_d1.0924234
X-RAY DIFFRACTIONf_dihedral_angle_d14.4266582
X-RAY DIFFRACTIONf_chiral_restr0.0412504
X-RAY DIFFRACTIONf_plane_restr0.0043128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.448-2.47580.26911460.15722605X-RAY DIFFRACTION87
2.4758-2.50490.26351250.16722642X-RAY DIFFRACTION89
2.5049-2.53550.27141310.16552614X-RAY DIFFRACTION87
2.5355-2.56760.26451430.15892650X-RAY DIFFRACTION88
2.5676-2.60140.26281510.15492659X-RAY DIFFRACTION90
2.6014-2.6370.22911530.14992690X-RAY DIFFRACTION90
2.637-2.67470.24921520.14662698X-RAY DIFFRACTION90
2.6747-2.71460.23551520.1462757X-RAY DIFFRACTION93
2.7146-2.7570.22151440.14352795X-RAY DIFFRACTION93
2.757-2.80220.24551340.14322811X-RAY DIFFRACTION95
2.8022-2.85050.24581590.14272879X-RAY DIFFRACTION96
2.8505-2.90230.24971680.14562843X-RAY DIFFRACTION96
2.9023-2.95820.22161520.14682915X-RAY DIFFRACTION97
2.9582-3.01850.21861440.14512947X-RAY DIFFRACTION98
3.0185-3.08420.20951540.13892974X-RAY DIFFRACTION99
3.0842-3.15590.22861570.13632974X-RAY DIFFRACTION99
3.1559-3.23480.21611630.13482991X-RAY DIFFRACTION100
3.2348-3.32220.20771660.12592979X-RAY DIFFRACTION100
3.3222-3.420.19191510.12453062X-RAY DIFFRACTION100
3.42-3.53030.19071880.11852957X-RAY DIFFRACTION100
3.5303-3.65650.1691550.1193011X-RAY DIFFRACTION100
3.6565-3.80280.20761430.12073067X-RAY DIFFRACTION100
3.8028-3.97580.15421590.11693020X-RAY DIFFRACTION100
3.9758-4.18530.15451400.11013068X-RAY DIFFRACTION100
4.1853-4.44740.17441420.10643046X-RAY DIFFRACTION100
4.4474-4.79050.15161760.1083065X-RAY DIFFRACTION100
4.7905-5.27210.18141490.11683056X-RAY DIFFRACTION100
5.2721-6.03380.18891630.14053105X-RAY DIFFRACTION100
6.0338-7.59730.20371680.15253118X-RAY DIFFRACTION100
7.5973-48.86830.171660.14853280X-RAY DIFFRACTION100

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