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- PDB-7qea: Crystal structure of fluorescein-di-Beta-D-glucuronide bound to a... -

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Basic information

Entry
Database: PDB / ID: 7qea
TitleCrystal structure of fluorescein-di-Beta-D-glucuronide bound to a mutant of SN243 (D415A)
ComponentsSN243
KeywordsHYDROLASE / enzyme discovery / carbohydrate-active enzymes (CAZy) / protein engineering / functional metagenomics)
Function / homologyACETATE ION / Chem-B9I
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsNeun, S. / Brear, P. / Campbell, E. / Omari, K. / Wagner, O. / Hyvonen, M. / Hollfelder, F.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)Metafluidics, 685474European Union
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Functional metagenomic screening identifies an unexpected beta-glucuronidase.
Authors: Neun, S. / Brear, P. / Campbell, E. / Tryfona, T. / El Omari, K. / Wagner, A. / Dupree, P. / Hyvonen, M. / Hollfelder, F.
History
DepositionDec 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SN243
B: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,69147
Polymers163,7462
Non-polymers3,94645
Water5,549308
1
A: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,16828
Polymers81,8731
Non-polymers2,29527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,52419
Polymers81,8731
Non-polymers1,65118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.268, 81.565, 93.393
Angle α, β, γ (deg.)66.640, 89.380, 89.570
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 785 or resid 831))
21(chain B and (resid 40 through 202 or resid 204...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 785 or resid 831))A40 - 354
121(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 785 or resid 831))A356 - 623
131(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 785 or resid 831))A625 - 785
141(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 785 or resid 831))A831
211(chain B and (resid 40 through 202 or resid 204...B40 - 202
221(chain B and (resid 40 through 202 or resid 204...B204 - 354
231(chain B and (resid 40 through 202 or resid 204...B356 - 623
241(chain B and (resid 40 through 202 or resid 204...B625 - 785
251(chain B and (resid 40 through 202 or resid 204...B831

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SN243


Mass: 81872.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic construct (others) / Plasmid: plasmid / Details (production host): pSol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3

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Non-polymers , 5 types, 353 molecules

#2: Chemical ChemComp-B9I / (2~{S},3~{S},4~{S},5~{R},6~{S})-3,4,5-tris(oxidanyl)-6-[(1~{R})-6'-oxidanyl-3-oxidanylidene-spiro[2-benzofuran-1,9'-xanthene]-3'-yl]oxy-oxane-2-carboxylic acid


Mass: 508.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H20O11 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 54.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 0.01 M ZnSO4 and 25% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.28→74.88 Å / Num. obs: 75860 / % possible obs: 97 % / Redundancy: 2.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.079 / Rrim(I) all: 0.124 / Net I/σ(I): 3.8 / Num. measured all: 171343 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.28-2.42.30.87625317111140.4520.7371.1510.897.2
7.21-74.882.20.045506823010.9930.0360.0589.393.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QE1

7qe1


Resolution: 2.28→51.113 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 3978 5.28 %
Rwork0.1982 71307 -
obs0.2012 75285 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.16 Å2 / Biso mean: 52.889 Å2 / Biso min: 24.27 Å2
Refinement stepCycle: final / Resolution: 2.28→51.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11223 0 136 308 11667
Biso mean--80.05 54 -
Num. residues----1476
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4506X-RAY DIFFRACTION4.98TORSIONAL
12B4506X-RAY DIFFRACTION4.98TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.28-2.30760.384980.321233887
2.3076-2.33680.37781100.3129249691
2.3368-2.36760.36521470.3042242895
2.3676-2.40.31721340.304257396
2.4-2.43430.35771430.2862253897
2.4343-2.47060.34611280.2778260297
2.4706-2.50920.31261570.2686254497
2.5092-2.55040.30621100.26260697
2.5504-2.59430.32661470.2531254497
2.5943-2.64150.29821280.2507262397
2.6415-2.69230.29691260.2477256998
2.6923-2.74730.33131390.2499265298
2.7473-2.8070.32191380.2472252597
2.807-2.87230.30941610.251257598
2.8723-2.94410.28691390.2292257398
2.9441-3.02370.28041320.2182261898
3.0237-3.11270.31831560.2199258498
3.1127-3.21310.27221520.2187252797
3.2131-3.3280.29891690.2053255696
3.328-3.46120.28112000.1984251498
3.4612-3.61870.24081470.183254998
3.6187-3.80940.2511470.1725258897
3.8094-4.0480.20771310.1502258397
4.048-4.36040.19821780.1451250197
4.3604-4.79890.17061390.1404257797
4.7989-5.49260.20071330.1564257396
5.4926-6.91730.25381400.1918250095
6.9173-51.1130.20071490.1878245193

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