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- PDB-4ean: 1.75A resolution structure of indole bound beta-glycosidase (W33G... -

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Basic information

Entry
Database: PDB / ID: 4ean
Title1.75A resolution structure of indole bound beta-glycosidase (W33G) from sulfolobus solfataricus
ComponentsBeta-galactosidase
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / Chemical biology / allosteric activation / switchable enzyme / chemical rescue
Function / homology
Function and homology information


beta-galactosidase / carbohydrate catabolic process / beta-galactosidase activity / 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
INDOLE / Beta-galactosidase
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsLovell, S. / Battaile, K.P. / Deckert, K. / Brunner, L.C. / Budiardjo, S.J. / Karanicolas, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Designing allosteric control into enzymes by chemical rescue of structure.
Authors: Deckert, K. / Budiardjo, S.J. / Brunner, L.C. / Lovell, S. / Karanicolas, J.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,94412
Polymers113,2602
Non-polymers68310
Water11,079615
1
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9726
Polymers56,6301
Non-polymers3425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9726
Polymers56,6301
Non-polymers3425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,94412
Polymers113,2602
Non-polymers68310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4950 Å2
ΔGint-79 kcal/mol
Surface area33490 Å2
MethodPISA
4
B: Beta-galactosidase
hetero molecules

B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,94412
Polymers113,2602
Non-polymers68310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4680 Å2
ΔGint-65 kcal/mol
Surface area33810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.544, 167.544, 95.232
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-824-

HOH

21B-795-

HOH

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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 P2 (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: lacS, SSO3019 / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P22498, beta-galactosidase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7N
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 45% MPD, 100 mM Bis-Tris, 200 mM Calcium Chloride, pH 6.5, VAPOR DIFFUSION, temperature 293K

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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: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 153873 / Num. obs: 153873 / % possible obs: 99.76 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.69 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.3765
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1.75-1.846.910.6515428022341199.95
1.84-1.966.70.4214170421165199.88
1.96-2.096.930.2513828419960199.99
2.09-2.266.860.1612747518580199.96
2.26-2.476.490.1211080917072199.73
2.47-2.776.80.0810528615492199.92
2.77-3.26.680.069150313703199.82
3.2-3.916.040.056938811493198.89
3.91-5.536.580.04597629079199.96
5.53-506.170.03307874988197.61

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.24 Å
Translation2.5 Å45.24 Å

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
PHASER2.3.0phasing
PHENIXdev_1011refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2CEQ

2ceq


Resolution: 1.75→33.932 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 7697 5.01 %RANDOM
Rwork0.1739 ---
obs0.1748 153499 99.49 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.985 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 84.96 Å2 / Biso mean: 24.9709 Å2 / Biso min: 10.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.3802 Å2-0 Å20 Å2
2---4.3802 Å20 Å2
3---8.7605 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7858 0 40 615 8513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018297
X-RAY DIFFRACTIONf_angle_d1.21111338
X-RAY DIFFRACTIONf_chiral_restr0.0771145
X-RAY DIFFRACTIONf_plane_restr0.0071474
X-RAY DIFFRACTIONf_dihedral_angle_d12.4442993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.76990.29522480.278748235071100
1.7699-1.79070.29432440.276848265070100
1.7907-1.81260.33992490.275648515100100
1.8126-1.83550.30082480.264349435191100
1.8355-1.85970.27942370.268748015038100
1.8597-1.88510.28152510.25344850510199
1.8851-1.91210.23742640.209548105074100
1.9121-1.94060.24022640.2148215085100
1.9406-1.97090.24612780.218948785156100
1.9709-2.00320.21032620.165547895051100
2.0032-2.03780.1732570.149748575114100
2.0378-2.07480.17872370.148349105147100
2.0748-2.11470.18013110.151248035114100
2.1147-2.15790.19362480.150248325080100
2.1579-2.20480.19442490.154749105159100
2.2048-2.25610.19872480.160248115059100
2.2561-2.31250.2052860.175948385124100
2.3125-2.3750.2192560.19344818507499
2.375-2.44490.2092360.16448845120100
2.4449-2.52370.18262500.157648455095100
2.5237-2.61390.15192390.136649035142100
2.6139-2.71850.16272600.134949135173100
2.7185-2.84220.15672580.14644801505999
2.8422-2.9920.19262400.155349325172100
2.992-3.17930.16972600.16734865512599
3.1793-3.42450.19212460.19514829507598
3.4245-3.76880.19262670.16584826509398
3.7688-4.31320.13192610.13649315192100
4.3132-5.43050.15342790.154349375216100
5.4305-33.93790.23782640.23334965522997
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4749-0.01830.13270.6236-0.01410.5781-0.04780.04870.348-0.041-0.01360.0456-0.1722-0.07880.04570.18180.0498-0.04180.14950.00790.266825.1708104.8604-5.3984
20.87850.11850.14110.57460.01030.4401-0.03010.14520.2488-0.0752-0.00320.0639-0.0604-0.03420.02370.17660.0398-0.0410.18510.0460.184319.141697.3941-17.1052
30.7758-0.17510.33990.6302-0.22040.56590.00070.14010.1297-0.0849-0.00910.00050.01510.0073-0.00930.14580.01230.00260.17270.02970.145536.017888.3936-13.9885
40.8447-0.09360.09030.6752-0.05560.32080.0808-0.0227-0.1908-0.0380.00390.07410.0635-0.0414-0.08370.17430.0271-0.0340.14530.01780.157345.274833.81768.5898
50.04980.0745-0.04990.7903-0.14090.96450.03480.0642-0.1706-0.0665-0.0456-0.13350.25520.240.01140.26180.0841-0.03830.227-0.00860.263659.255722.17783.1296
60.6409-0.15030.080.3205-0.080.45790.09810.018-0.17560.0204-0.00910.11760.1001-0.0647-0.07550.2550.0327-0.07050.17780.01730.263351.291719.52197.2761
70.36990.2720.0751.0286-0.01150.39060.09350.0488-0.1464-0.0965-0.0591-0.05830.12240.0782-0.03390.18990.0742-0.02920.1544-0.00870.160162.108429.29990.4463
80.8957-0.335-0.00891.2653-0.05930.49190.17580.26450.0362-0.3045-0.013-0.16750.07110.1252-0.12530.28020.07750.01620.249-0.03280.171857.052233.9201-15.7094
90.9261-0.4421-0.00290.96120.11130.42780.09760.1097-0.0005-0.1184-0.0553-0.04850.03320.043-0.04020.16410.0327-0.02910.15310.00980.116143.711342.8538-8.368
100.8071-0.20520.30840.7635-0.1750.68110.0189-0.0061-0.076-0.08560.01470.0820.0061-0.0818-0.03220.14570.0174-0.04350.17840.01440.174629.573742.2346-1.3165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:159 )A1 - 159
2X-RAY DIFFRACTION2( CHAIN A AND RESID 160:285 )A160 - 285
3X-RAY DIFFRACTION3( CHAIN A AND RESID 286:489 )A286 - 489
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:72 )B1 - 72
5X-RAY DIFFRACTION5( CHAIN B AND RESID 73:111 )B73 - 111
6X-RAY DIFFRACTION6( CHAIN B AND RESID 112:159 )B112 - 159
7X-RAY DIFFRACTION7( CHAIN B AND RESID 160:253 )B160 - 253
8X-RAY DIFFRACTION8( CHAIN B AND RESID 254:321 )B254 - 321
9X-RAY DIFFRACTION9( CHAIN B AND RESID 322:446 )B322 - 446
10X-RAY DIFFRACTION10( CHAIN B AND RESID 447:489 )B447 - 489

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