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- PDB-4eam: 1.70A resolution structure of apo beta-glycosidase (W33G) from su... -

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Basic information

Entry
Database: PDB / ID: 4eam
Title1.70A resolution structure of apo 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 / 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 P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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)114,42716
Polymers113,2602
Non-polymers1,16614
Water12,917717
1
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2138
Polymers56,6301
Non-polymers5837
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2138
Polymers56,6301
Non-polymers5837
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)114,42716
Polymers113,2602
Non-polymers1,16614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6170 Å2
ΔGint-134 kcal/mol
Surface area32910 Å2
MethodPISA
4
B: Beta-galactosidase
hetero molecules

B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,42716
Polymers113,2602
Non-polymers1,16614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6210 Å2
ΔGint-137 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.700, 167.700, 96.398
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-899-

HOH

21B-963-

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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 3.45 Å3/Da / Density % sol: 64.4 %
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: 1.7→50 Å / Num. all: 170417 / Num. obs: 170417 / % possible obs: 99.89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.75 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.6094
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1.7-1.797.110.63175867247471100
1.79-1.96.880.4316123423433199.99
1.9-2.036.870.2615156422050199.99
2.03-2.196.950.17142970205771100
2.19-2.46.610.1212507818924199.98
2.4-2.696.750.0911582017167199.95
2.69-3.16.790.0710276115131199.97
3.1-3.85.960.067638112805199.53
3.8-5.386.530.046547310033199.88
5.38-506.090.04338185550198.41

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.41 Å
Translation2.5 Å48.41 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: 1.7→34.156 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.14 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.186 8526 5.01 %RANDOM
Rwork0.168 ---
obs0.1689 170140 99.74 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.775 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 84.6 Å2 / Biso mean: 21.6055 Å2 / Biso min: 8.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.2431 Å20 Å20 Å2
2---2.2431 Å20 Å2
3---4.4863 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7826 0 70 717 8613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018305
X-RAY DIFFRACTIONf_angle_d1.22711361
X-RAY DIFFRACTIONf_chiral_restr0.0791152
X-RAY DIFFRACTIONf_plane_restr0.0071472
X-RAY DIFFRACTIONf_dihedral_angle_d12.5243008
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 (%)
1.7-1.71930.31162830.33353525635100
1.7193-1.73960.34582720.319853745646100
1.7396-1.76080.30662860.28753805666100
1.7608-1.78310.31052470.277353575604100
1.7831-1.80650.25072970.254253665663100
1.8065-1.83130.25872690.250153495618100
1.8313-1.85740.25772980.245653745672100
1.8574-1.88520.27242990.239253325631100
1.8852-1.91460.20072800.183553955675100
1.9146-1.9460.20712980.178253365634100
1.946-1.97960.22222720.185653785650100
1.9796-2.01550.17683000.147854035703100
2.0155-2.05430.1762620.143753855647100
2.0543-2.09620.16382270.144554175644100
2.0962-2.14180.17432760.142353915667100
2.1418-2.19160.17342930.142653385631100
2.1916-2.24640.16943010.142353685669100
2.2464-2.30710.17292930.146153695662100
2.3071-2.3750.19182720.169553725644100
2.375-2.45170.15252790.135653915670100
2.4517-2.53930.15562790.144553885667100
2.5393-2.64090.15573030.129254005703100
2.6409-2.7610.15862980.139453815679100
2.761-2.90650.15712510.142254345685100
2.9065-3.08850.16422980.151353885686100
3.0885-3.32680.21893070.1865373568099
3.3268-3.66120.16643270.17365375570299
3.6612-4.19020.17493000.13715417571799
4.1902-5.27610.15172790.134754875766100
5.2761-34.16340.21452800.22835544582498
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)
10.89840.2353-0.21781.0863-0.09850.46360.06910.05940.1730.09850.01450.0926-0.0496-0.0476-0.09250.09630.0050.03940.15240.0170.12336.7385-55.979424.8743
20.6236-0.47140.0270.55010.36441.23130.03370.0715-0.1064-0.0043-0.10240.12270.1078-0.31720.08780.12860.00310.02560.24120.00950.1867-9.851-62.046919.6982
33.24372.1469-0.95841.8553-0.29860.97190.1313-0.08240.28610.0531-0.05990.116-0.0642-0.0674-0.07470.150.05360.06630.19730.02550.2396-12.6405-51.112826.0043
40.8035-0.72960.0241.2604-0.02850.12230.02270.11780.01840.0537-0.00290.0573-0.0396-0.0706-0.02820.1183-0.00230.02530.21420.02030.1387-4.3247-66.105219.4533
50.925-0.2386-0.22370.98030.21290.44860.01230.2996-0.0532-0.07970.04190.0805-0.0022-0.0947-0.06060.1090.0048-0.0070.25020.02180.097-2.4456-66.44187.2743
65.6997-0.7495-0.11311.74670.0441.56350.06490.7032-0.5372-0.2013-0.01620.03560.0992-0.1869-0.0150.1912-0.0344-0.0140.3257-0.04270.1244-0.5872-70.5781-1.6552
73.0136-0.14670.23950.7298-0.19690.40130.16370.2462-0.4663-0.1781-0.0119-0.00730.0964-0.0676-0.12930.16810.0032-0.00350.2113-0.01650.163610.618-67.91813.9238
80.69290.2417-0.15310.34130.03870.10720.02420.15310.0758-0.02570.0215-0.001-0.0273-0.0368-0.0420.12470.00750.04040.17750.03820.12914.6933-55.449711.0722
92.7347-0.8713-0.05651.09880.57170.6410.05560.13010.0829-0.0701-0.03090.0311-0.0716-0.0232-0.03020.1261-0.0180.05410.15270.05770.167423.3197-45.92099.1025
100.89350.30550.1360.7593-0.09810.4595-0.011-0.009-0.15140.0433-0.0096-0.1756-0.00510.0870.00780.0986-0.00830.00160.14430.02150.131870.5466-74.410215.5403
111.316-0.1569-0.38250.158-0.23371.49950.03010.08240.0526-0.0996-0.0829-0.3255-0.19340.3090.08520.14-0.00950.03510.1920.02680.239184.0005-69.84934.0583
123.81051.6595-0.63770.92580.05051.3050.0093-0.005-0.12530.0002-0.0683-0.46420.08220.36440.04450.11790.04490.00990.27330.08410.388889.0767-79.702711.2268
130.487-0.214-0.27291.8616-0.08820.3063-0.0090.0163-0.0416-0.0118-0.0303-0.24490.0090.08480.03610.1059-0.00740.00570.17340.01670.162378.7713-65.9344.9301
141.5230.0739-0.27871.1246-0.24050.5231-0.02720.2440.0392-0.17550.0284-0.08410.0080.0094-0.00290.1556-0.01230.03590.1668-0.00550.089669.3776-66.8163-7.4621
151.5394-0.1414-0.66340.62320.01680.81060.10360.17670.1706-0.17570.0114-0.085-0.0811-0.0377-0.10890.1596-0.01180.0240.13540.010.120561.0209-66.6214-4.8499
160.51260.261-0.11470.5111-0.27740.4564-0.04910.0492-0.088-0.0780.0068-0.08690.0364-0.00750.04630.1136-0.00560.00450.1198-0.02170.125557.5115-80.82546.2676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:72 )A1 - 72
2X-RAY DIFFRACTION2( CHAIN A AND RESID 73:111 )A73 - 111
3X-RAY DIFFRACTION3( CHAIN A AND RESID 112:140 )A112 - 140
4X-RAY DIFFRACTION4( CHAIN A AND RESID 141:228 )A141 - 228
5X-RAY DIFFRACTION5( CHAIN A AND RESID 229:274 )A229 - 274
6X-RAY DIFFRACTION6( CHAIN A AND RESID 275:309 )A275 - 309
7X-RAY DIFFRACTION7( CHAIN A AND RESID 310:346 )A310 - 346
8X-RAY DIFFRACTION8( CHAIN A AND RESID 347:456 )A347 - 456
9X-RAY DIFFRACTION9( CHAIN A AND RESID 457:489 )A457 - 489
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1:72 )B1 - 72
11X-RAY DIFFRACTION11( CHAIN B AND RESID 73:111 )B73 - 111
12X-RAY DIFFRACTION12( CHAIN B AND RESID 112:140 )B112 - 140
13X-RAY DIFFRACTION13( CHAIN B AND RESID 141:228 )B141 - 228
14X-RAY DIFFRACTION14( CHAIN B AND RESID 229:285 )B229 - 285
15X-RAY DIFFRACTION15( CHAIN B AND RESID 286:364 )B286 - 364
16X-RAY DIFFRACTION16( CHAIN B AND RESID 365:489 )B365 - 489

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