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- PDB-7brs: E.coli beta-galactosidase (E537Q) in complex with fluorescent pro... -

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Basic information

Entry
Database: PDB / ID: 7brs
TitleE.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA02
ComponentsBeta-galactosidase
KeywordsHYDROLASE / beta_galactosidase / fluorescent probe
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / : / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site ...Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / : / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / 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 / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-F4X / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsChen, X. / Hu, Y.L. / Gao, Y. / Yuan, R. / Guo, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977082, 21472148, 21807088, 81872747 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Two-Dimensional Design Strategy to Construct Smart Fluorescent Probes for the Precise Tracking of Senescence.
Authors: Gao, Y. / Hu, Y. / Liu, Q. / Li, X. / Li, X. / Kim, C.Y. / James, T.D. / Li, J. / Chen, X. / Guo, Y.
History
DepositionMar 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)473,07070
Polymers466,7544
Non-polymers6,31666
Water6,882382
1
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,59321
Polymers116,6891
Non-polymers1,90420
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,13316
Polymers116,6891
Non-polymers1,44515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,28918
Polymers116,6891
Non-polymers1,60117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,05515
Polymers116,6891
Non-polymers1,36614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)246.653, 84.423, 240.650
Angle α, β, γ (deg.)90.000, 94.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-galactosidase / Beta-gal / Lactase


Mass: 116688.547 Da / Num. of mol.: 4 / Mutation: E537Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: lacZ, b0344, JW0335 / Production host: Escherichia coli (E. coli) / References: UniProt: P00722, beta-galactosidase

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Non-polymers , 6 types, 448 molecules

#2: Chemical
ChemComp-F4X / 8-[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-indol-1-ium-1-yl]octanoic acid


Mass: 568.678 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H42NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 100mM Bis-Tris, pH=5.9, 200mM NaCl, 200mM MgCl2, 10% PEG8000, 10% glycerol, 0.1M guanidine hydrochloride, 10mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→30.04 Å / Num. obs: 140020 / % possible obs: 99.6 % / Redundancy: 1 % / CC1/2: 0.87 / Rpim(I) all: 0.068 / Rrim(I) all: 0.156 / Net I/σ(I): 12.7
Reflection shellResolution: 2.67→2.72 Å / Redundancy: 1 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6908 / CC1/2: 0.87 / CC star: 0.965 / Rpim(I) all: 0.307 / Rrim(I) all: 0.701 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KUZ

6kuz


Resolution: 2.67→30.04 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 6843 4.89 %
Rwork0.2003 133129 -
obs0.2024 139972 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.68 Å2 / Biso mean: 69.9823 Å2 / Biso min: 11.57 Å2
Refinement stepCycle: final / Resolution: 2.67→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31727 0 369 382 32478
Biso mean--75.26 44.21 -
Num. residues----4063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.67-2.70030.34452320.2832432399
2.7003-2.73210.31682150.268441899
2.7321-2.76540.30222370.2648437699
2.7654-2.80040.32632630.2604437599
2.8004-2.83720.30752260.25374389100
2.8372-2.8760.32072100.24824404100
2.876-2.91710.30192450.23534409100
2.9171-2.96060.2832190.23784424100
2.9606-3.00680.30342240.23934399100
3.0068-3.05610.28612230.23464422100
3.0561-3.10870.2972300.23544440100
3.1087-3.16520.26642220.21734428100
3.1652-3.2260.27122180.2174397100
3.226-3.29170.27852300.2194415100
3.2917-3.36320.22542310.2024461100
3.3632-3.44140.25542410.2154422100
3.4414-3.52730.23682060.20034471100
3.5273-3.62250.24782290.20274405100
3.6225-3.72890.22912280.19244455100
3.7289-3.8490.21742370.18744439100
3.849-3.98630.22382320.18914422100
3.9863-4.14550.22582230.18044450100
4.1455-4.33370.21672520.17524435100
4.3337-4.56140.19942390.15814410100
4.5614-4.84610.21952260.16244491100
4.8461-5.21850.23932090.18234518100
5.2185-5.74030.20812140.1894440898
5.7403-6.56340.26852220.2034543100
6.5634-8.24080.21262370.18824522100
8.2408-30.040.21542230.18784658100
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)
11.0918-0.09360.4957-0.2306-0.07542.0233-0.016-0.40980.07680.0134-0.2202-0.14990.7284-1.06340.16370.9434-0.35820.18050.5964-0.23680.3672-15.8481-42.568734.0602
21.0720.0003-0.8176-0.16070.06882.06760.10030.5873-0.12310.0244-0.2353-0.15-0.697-1.09060.07760.80880.3572-0.01560.7107-0.2040.3267-19.385-13.794383.945
30.8967-0.06260.63310.1851-0.05711.9064-0.2737-0.42290.3680.0353-0.1610.056-0.1441-0.97350.34910.54480.0834-0.02520.6851-0.38570.6253-36.2727-18.4151-9.8235
41.4270.0427-0.92970.2842-0.13021.7198-0.23820.6798-0.57530.0249-0.16220.11820.183-0.92910.29660.4094-0.07840.02550.6994-0.42460.6826-46.607-38.0052124.2866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 4:1201)A4 - 1201
2X-RAY DIFFRACTION2(chain B and resseq 4:1102)B4 - 1102
3X-RAY DIFFRACTION3(chain C and resseq 4:1102)C4 - 1102
4X-RAY DIFFRACTION4(chain D and resseq 4:1102)D4 - 1102

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