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- PDB-4ze5: Structure of Gan1D-E170Q, a catalytic mutant of a putative 6-phos... -

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Basic information

Entry
Database: PDB / ID: 4ze5
TitleStructure of Gan1D-E170Q, a catalytic mutant of a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / TIM-barrel / catalytic mutant / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLansky, S. / Zehavi, A. / Dvir, H. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Structure of Gan1D-E170Q, a catalytic mutant of 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 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.title / _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
C: Putative 6-phospho-beta-galactobiosidase
D: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,96317
Polymers224,8354
Non-polymers1,12813
Water46,0462556
1
D: Putative 6-phospho-beta-galactobiosidase
hetero molecules

A: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0169
Polymers112,4172
Non-polymers5997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
MethodPISA
2
C: Putative 6-phospho-beta-galactobiosidase
hetero molecules

B: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9478
Polymers112,4172
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
MethodPISA
3
A: Putative 6-phospho-beta-galactobiosidase
hetero molecules

D: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0169
Polymers112,4172
Non-polymers5997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area4800 Å2
ΔGint-12 kcal/mol
Surface area32020 Å2
MethodPISA
4
B: Putative 6-phospho-beta-galactobiosidase
hetero molecules

C: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9478
Polymers112,4172
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area4480 Å2
ΔGint-15 kcal/mol
Surface area31820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.550, 97.440, 105.240
Angle α, β, γ (deg.)90.00, 97.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 56208.730 Da / Num. of mol.: 4
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.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2556 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-18% PEG 8K, 3% MPD, 0.1 M imidazole buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.48→35 Å / Num. obs: 337040 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.6
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 5 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.9 / % possible all: 94.9

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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: 1.48→27.64 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.858 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15929 16966 5 %RANDOM
Rwork0.1321 ---
obs0.13346 319084 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.232 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å20.17 Å2
2--0.63 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.48→27.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15110 0 75 2556 17741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.01916309
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214814
X-RAY DIFFRACTIONr_angle_refined_deg2.5041.92722286
X-RAY DIFFRACTIONr_angle_other_deg1.055334023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97252002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19723.45913
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.911152566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0515135
X-RAY DIFFRACTIONr_chiral_restr0.1560.22226
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02118972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024273
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_it1.7941.1187551
X-RAY DIFFRACTIONr_mcbond_other1.7941.1187550
X-RAY DIFFRACTIONr_mcangle_it2.731.6729467
X-RAY DIFFRACTIONr_mcangle_other2.731.6729468
X-RAY DIFFRACTIONr_scbond_it2.8941.3958758
X-RAY DIFFRACTIONr_scbond_other2.8941.3958759
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3232.00112739
X-RAY DIFFRACTIONr_long_range_B_refined7.12611.71222123
X-RAY DIFFRACTIONr_long_range_B_other7.12611.71322124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 1195 -
Rwork0.215 22768 -
obs--96.55 %

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