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- PDB-5ixe: 1.75A RESOLUTION STRUCTURE OF 5-Fluoroindole BOUND BETA-GLYCOSIDA... -

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Basic information

Entry
Database: PDB / ID: 5ixe
Title1.75A RESOLUTION STRUCTURE OF 5-Fluoroindole BOUND BETA-GLYCOSIDASE (W33G) FROM SULFOLOBUS SOLFATARICUS
ComponentsBeta-galactosidase
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / ALLOSTERIC ACTIVATION / SWITCHABLE ENZYME / CHEMICAL RESCUE
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
5-fluoro-1H-indole / Beta-galactosidase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Budiardjo, S.J. / Karanicolas, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB130049 United States
CitationJournal: ACS Synth Biol / Year: 2016
Title: Full and Partial Agonism of a Designed Enzyme Switch.
Authors: Budiardjo, S.J. / Licknack, T.J. / Cory, M.B. / Kapros, D. / Roy, A. / Lovell, S. / Douglas, J. / Karanicolas, J.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _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: Beta-galactosidase
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,86211
Polymers113,2602
Non-polymers6019
Water10,233568
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,98012
Polymers113,2602
Non-polymers71910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3950 Å2
ΔGint-82 kcal/mol
Surface area33530 Å2
MethodPISA
2
A: Beta-galactosidase
hetero molecules

B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,86211
Polymers113,2602
Non-polymers6019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2810 Å2
ΔGint-68 kcal/mol
Surface area34710 Å2
MethodPISA
3
B: Beta-galactosidase
hetero molecules

B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,74310
Polymers113,2602
Non-polymers4838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3380 Å2
ΔGint-67 kcal/mol
Surface area34190 Å2
MethodPISA
4
A: Beta-galactosidase
B: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,72322
Polymers226,5214
Non-polymers1,20218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area11250 Å2
ΔGint-161 kcal/mol
Surface area63790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.706, 167.706, 95.871
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Beta-galactosidase / Lactase


Mass: 56630.230 Da / Num. of mol.: 2 / Mutation: W33G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: lacS, SSO3019 / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(2DE3) pLysS / References: UniProt: P22498, beta-galactosidase
#2: Chemical ChemComp-14O / 5-fluoro-1H-indole


Mass: 135.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6FN
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 3.44 Å3/Da / Density % sol: 64.21 % / Description: Colorless prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 45% 2,-methyl-2,4-pentanediol, 100 mM Bis-Tris, 200 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→48.41 Å / Num. obs: 155679 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 23.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 10.7 / Num. measured all: 1526719 / Scaling rejects: 39
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.75-1.7810.11.1621100
9.59-48.419.80.04199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.45 Å83.83 Å
Translation8.45 Å83.83 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIX(dev_2026)refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EAN

4ean


Resolution: 1.75→34.063 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 18.94
RfactorNum. reflection% reflection
Rfree0.1728 7720 4.96 %
Rwork0.1527 --
obs0.1537 155583 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.67 Å2 / Biso mean: 29.8072 Å2 / Biso min: 15.06 Å2
Refinement stepCycle: final / Resolution: 1.75→34.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7854 0 34 568 8456
Biso mean--42.69 38.69 -
Num. residues----973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098294
X-RAY DIFFRACTIONf_angle_d1.00611341
X-RAY DIFFRACTIONf_chiral_restr0.0581147
X-RAY DIFFRACTIONf_plane_restr0.0071476
X-RAY DIFFRACTIONf_dihedral_angle_d12.1712981
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.76990.3122590.269149235182
1.7699-1.79070.28871930.252749445137
1.7907-1.81260.29442800.247348705150
1.8126-1.83550.26543060.234448105116
1.8355-1.85970.24842560.225849425198
1.8597-1.88510.22482730.209748825155
1.8851-1.91210.21342280.196949385166
1.9121-1.94060.20492790.190148225101
1.9406-1.97090.23092740.189849195193
1.9709-2.00320.20992690.181648725141
2.0032-2.03780.22292900.17648855175
2.0378-2.07480.19382600.169649055165
2.0748-2.11470.18762160.165349125128
2.1147-2.15790.1892750.164648935168
2.1579-2.20480.19322700.161649195189
2.2048-2.25610.18552440.152548895133
2.2561-2.31250.1792620.15149245186
2.3125-2.3750.1632400.143249265166
2.375-2.44480.17442310.143549685199
2.4448-2.52370.16072760.139249115187
2.5237-2.61390.15312650.133549305195
2.6139-2.71850.15982750.13949035178
2.7185-2.84220.1742190.144349715190
2.8422-2.99190.16652560.141549445200
2.9919-3.17930.15992690.138249205189
3.1793-3.42450.14472600.138549645224
3.4245-3.76880.12992200.133549905210
3.7688-4.31320.14742350.122450315266
4.3132-5.43060.162690.137149945263
5.4306-34.06940.16942710.173951625433

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