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

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Basic information

Entry
Database: PDB / ID: 7btk
TitleE.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA01
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 / Glycosyl hydrolases family 2 signature 1. ...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 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / 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-F6L / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, X. / Hu, Y.L. / Liu, Q.M. / Gao, Y. / Yuan, R. / Guo, Y.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977082 China
National Natural Science Foundation of China (NSFC)21472148 China
National Natural Science Foundation of China (NSFC)21807088 China
National Natural Science Foundation of China (NSFC)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
DepositionApr 1, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,38961
Polymers466,7544
Non-polymers5,63557
Water20,2491124
1
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,28118
Polymers116,6891
Non-polymers1,59317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,17015
Polymers116,6891
Non-polymers1,48114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,96914
Polymers116,6891
Non-polymers1,28013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,96914
Polymers116,6891
Non-polymers1,28013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)249.832, 85.454, 243.307
Angle α, β, γ (deg.)90.000, 94.150, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA3 - 10235 - 1025
21LYSLYSBB3 - 10235 - 1025
12GLNGLNAA3 - 10225 - 1024
22GLNGLNCC3 - 10225 - 1024
13LYSLYSAA3 - 10235 - 1025
23LYSLYSDD3 - 10235 - 1025
14GLNGLNBB3 - 10225 - 1024
24GLNGLNCC3 - 10225 - 1024
15LYSLYSBB3 - 10235 - 1025
25LYSLYSDD3 - 10235 - 1025
16GLNGLNCC3 - 10225 - 1024
26GLNGLNDD3 - 10225 - 1024

NCS ensembles :
ID
1
2
3
4
5
6

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00722, beta-galactosidase

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Non-polymers , 6 types, 1181 molecules

#2: Chemical
ChemComp-F6L / 4-[[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-2H-indol-1-yl]methyl]benzoic acid


Mass: 560.614 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H34NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / 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 / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 1124 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 100 mM Bis-Tris, pH = 5.9, 200 mM NaCl, 200 mM MgCl2, 10% PEG8000, 10% glycerol, 0.1 M guanidine hydrochloride and 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→19.87 Å / Num. obs: 140397 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.068 / Rrim(I) all: 0.178 / Net I/σ(I): 9.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 6952 / CC1/2: 0.838 / Rpim(I) all: 0.423 / Rrim(I) all: 0.797 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KUZ

6kuz


Resolution: 2.7→19.87 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.958 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 7202 5.1 %RANDOM
Rwork0.2177 ---
obs0.2185 133155 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.07 Å2 / Biso mean: 35.665 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.71 Å20 Å20.89 Å2
2---0.69 Å20 Å2
3----3.11 Å2
Refinement stepCycle: final / Resolution: 2.7→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32402 0 336 1124 33862
Biso mean--84.72 25.54 -
Num. residues----4086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01433677
X-RAY DIFFRACTIONr_bond_other_d0.0010.01728466
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.66145950
X-RAY DIFFRACTIONr_angle_other_deg1.0891.64366626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08754084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89121.8291935
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.391155003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.59715254
X-RAY DIFFRACTIONr_chiral_restr0.0560.24228
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0238501
X-RAY DIFFRACTIONr_gen_planes_other0.0040.026595
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A336240.08
12B336240.08
21A332420.09
22C332420.09
31A332040.1
32D332040.1
41B332070.1
42C332070.1
51B331280.1
52D331280.1
61C334100.09
62D334100.09
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 552 -
Rwork0.292 9781 -
all-10333 -
obs--99.52 %

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