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- PDB-6kuz: E.coli beta-galactosidase (E537Q) in complex with fluorescent pro... -

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Basic information

Entry
Database: PDB / ID: 6kuz
TitleE.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSL01
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-DVL / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsChen, X. / Hu, Y.L. / Li, X.K. / Guo, Y. / Li, J.
CitationJournal: Chem Sci / Year: 2020
Title: First-generation species-selective chemical probes for fluorescence imaging of human senescence-associated beta-galactosidase.
Authors: Li, X. / Qiu, W. / Li, J. / Chen, X. / Hu, Y. / Gao, Y. / Shi, D. / Li, X. / Lin, H. / Hu, Z. / Dong, G. / Sheng, C. / Jiang, B. / Xia, C. / Kim, C.Y. / Guo, Y. / Li, J.
History
DepositionSep 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Nov 22, 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

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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)471,85364
Polymers466,4064
Non-polymers5,44760
Water8,233457
1
A: Beta-galactosidase
B: Beta-galactosidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)472,30870
Polymers466,4064
Non-polymers5,90266
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area27790 Å2
ΔGint-130 kcal/mol
Surface area135020 Å2
MethodPISA
2
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules

C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,39858
Polymers466,4064
Non-polymers4,99354
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area25160 Å2
ΔGint-166 kcal/mol
Surface area133920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.174, 85.506, 243.052
Angle α, β, γ (deg.)90.000, 94.090, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 116601.484 Da / Num. of mol.: 4 / Mutation: E537Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: lacZ, b0344, JW0335 / Production host: Escherichia coli (E. coli) / References: UniProt: P00722, beta-galactosidase

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Non-polymers , 6 types, 517 molecules

#2: Chemical
ChemComp-DVL / 3-(1,3-benzothiazol-2-yl)-2-[[4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]methoxy]-5-methyl-benzaldehyde


Mass: 537.581 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H27NO8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#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.: 457 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 10% PEG8000, 100mM Bis-Tris ph5,9, 200mM Nacl, 10mM DTT, 0.1M Guanidine Hydrochloride 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.83→29.5 Å / Num. obs: 118019 / % possible obs: 97.1 % / Redundancy: 1.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.082 / Rrim(I) all: 0.163 / Net I/av σ(I): 8.8 / Net I/σ(I): 6.7
Reflection shellResolution: 2.83→2.88 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5767 / CC1/2: 0.953 / Rpim(I) all: 0.22 / Rrim(I) all: 0.447 / % possible all: 96.7
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC7.0.076refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F4H

1f4h


Resolution: 2.83→29.5 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22431 5871 5 %RANDOM
Rwork0.18168 ---
obs0.18381 112147 96.9 %-
Displacement parametersBiso mean: 36.566 Å2
Refinement stepCycle: LAST / Resolution: 2.83→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32401 0 318 457 33176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012533705
X-RAY DIFFRACTIONf_angle_d1.449546008
X-RAY DIFFRACTIONf_chiral_restr0.07764822
X-RAY DIFFRACTIONf_plane_restr0.00576035
X-RAY DIFFRACTIONf_dihedral_angle_d16.000119522
LS refinement shellResolution: 2.83→2.904 Å
RfactorNum. reflection% reflection
Rfree0.296 418 -
Rwork0.271 --
obs--96.8 %

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