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- PDB-1uwi: CRYSTAL STRUCTURE OF MUTATED BETA-GLYCOSIDASE FROM SULFOLOBUS SOL... -

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Basic information

Entry
Database: PDB / ID: 1uwi
TitleCRYSTAL STRUCTURE OF MUTATED BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS, WORKING AT MODERATE TEMPERATURE
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / BETA-GLYCOSIDASE / GLYCOSIDASE
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process
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 ...: / 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
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsIsorna, P. / Polaina, J. / Sanz-Aparicio, J.
CitationJournal: Protein J. / Year: 2007
Title: Comparative Study and Mutational Analysis of Distinctive Structural Elements of Hyperthermophilic Enzymes.
Authors: Leon, M. / Isorna, P. / Menendez, M. / Sanz-Aparicio, J. / Polaina, J.
History
DepositionFeb 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
D: BETA-GALACTOSIDASE


Theoretical massNumber of molelcules
Total (without water)226,8974
Polymers226,8974
Non-polymers00
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.082, 132.425, 219.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.40078, 0.21908, -0.88959), (0.22797, -0.9166, -0.32844), (-0.88736, -0.33443, 0.31741)53.07684, 153.48093, 74.22582
2given(-0.61721, 0.65388, 0.43759), (0.66704, 0.13992, 0.73177), (0.41726, 0.74354, -0.52253)-75.12876, 3.08905, 62.43442
3given(0.01162, -0.88758, 0.46051), (-0.88412, -0.22426, -0.40992), (0.46711, -0.40238, -0.78734)26.50371, 114.4352, 159.37268

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Components

#1: Protein
BETA-GALACTOSIDASE / GLYCOSIDASE / LACTASE


Mass: 56724.223 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: DELTA-PUC18 / Production host: ESCHERICHIA COLI DH5[ALPHA] (bacteria) / References: UniProt: P22498, beta-galactosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 45 %
Crystal growpH: 9
Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 4K, 0.2 M NACL, PH=9, pH 9.00

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 15, 2003 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→41.2 Å / Num. obs: 75479 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 3.5
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOW

1gow


Resolution: 2.55→28.44 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1340044.71 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: LOOPS 93-98, 300-304, 329-333 HAVE BEEN EXCLUDED FROM THE NCS RESTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 5325 7.1 %RANDOM
Rwork0.209 ---
obs0.209 75141 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.3751 Å2 / ksol: 0.393791 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å20 Å2
2---2.95 Å20 Å2
3---5.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.55→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16068 0 0 426 16494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.482.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 875 7 %
Rwork0.269 11568 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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