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- PDB-4ypj: X-ray Structure of The Mutant of Glycoside Hydrolase -

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Basic information

Entry
Database: PDB / ID: 4ypj
TitleX-ray Structure of The Mutant of Glycoside Hydrolase
ComponentsBeta galactosidase
KeywordsHYDROLASE / Glycoside Hydrolase
Function / homology
Function and homology information


beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
: / Beta-galactosidase-like, Galactose-binding domain / Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Invasin/intimin cell-adhesion fragments ...: / Beta-galactosidase-like, Galactose-binding domain / Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsIshikawa, K. / Kataoka, M. / Yanamoto, T. / Nakabayashi, M. / Watanabe, M.
CitationJournal: Febs J. / Year: 2015
Title: Crystal structure of beta-galactosidase from Bacillus circulans ATCC 31382 (BgaD) and the construction of the thermophilic mutants.
Authors: Ishikawa, K. / Kataoka, M. / Yanamoto, T. / Nakabayashi, M. / Watanabe, M. / Ishihara, S. / Yamaguchi, S.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2May 31, 2017Group: Structure summary
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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


Theoretical massNumber of molelcules
Total (without water)181,7522
Polymers181,7522
Non-polymers00
Water16,574920
1
A: Beta galactosidase


Theoretical massNumber of molelcules
Total (without water)90,8761
Polymers90,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta galactosidase


Theoretical massNumber of molelcules
Total (without water)90,8761
Polymers90,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.415, 161.415, 275.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-1130-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 38 - 847 / Label seq-ID: 1 - 810

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Beta galactosidase


Mass: 90875.875 Da / Num. of mol.: 2 / Fragment: UNP residues 38-847 / Mutation: C-terminal truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: bga / Production host: Escherichia coli (E. coli) / References: UniProt: E5RWQ2, beta-galactosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 920 / 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: 4.93 Å3/Da / Density % sol: 75.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: sodium citrate tribasic dihydrate, sodium acetate trihydrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 124740 / % possible obs: 98.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 13.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.9 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPmodel building
RefinementResolution: 2.5→29.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.507 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19783 6246 5 %RANDOM
Rwork0.16297 ---
obs0.16471 118096 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.863 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.5→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12844 0 0 920 13764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01913160
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212082
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9317854
X-RAY DIFFRACTIONr_angle_other_deg1.19327828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19651618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58524.562640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.388152162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5291564
X-RAY DIFFRACTIONr_chiral_restr0.0980.21898
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215116
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023128
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_it2.3192.8976478
X-RAY DIFFRACTIONr_mcbond_other2.3172.8966477
X-RAY DIFFRACTIONr_mcangle_it3.5674.3388094
X-RAY DIFFRACTIONr_mcangle_other3.5674.3398095
X-RAY DIFFRACTIONr_scbond_it3.323.1856682
X-RAY DIFFRACTIONr_scbond_other3.323.1856682
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2514.6279760
X-RAY DIFFRACTIONr_long_range_B_refined6.65722.84615692
X-RAY DIFFRACTIONr_long_range_B_other6.60422.80515335
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 48846 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 441 -
Rwork0.302 8343 -
obs--95.85 %

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