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- PDB-7qef: Crystal structure of para-nitrophenyl-Beta-D-glucuronide bound to... -

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Basic information

Entry
Database: PDB / ID: 7qef
TitleCrystal structure of para-nitrophenyl-Beta-D-glucuronide bound to a mutant of SN243 (D415A)
ComponentsSN243
KeywordsHYDROLASE / enzyme discovery / carbohydrate-active enzymes (CAZy) / protein engineering / functional metagenomics)
Function / homologyGlycoside hydrolase, family 3, N-terminal domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / ACETATE ION / 4-nitrophenyl beta-D-glucopyranosiduronic acid
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsNeun, S. / Brear, P. / Campbell, E. / Omari, K. / Wagner, O. / Hyvonen, M. / Hollfelder, F.
Funding support1items
OrganizationGrant numberCountry
European Union (EU)Metafluidics, 685474
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 2, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)167,30547
Polymers163,7462
Non-polymers3,55945
Water3,027168
1
A: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,97428
Polymers81,8731
Non-polymers2,10127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,33119
Polymers81,8731
Non-polymers1,45818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.376, 81.675, 93.548
Angle α, β, γ (deg.)66.570, 89.390, 89.170
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 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 831))A40 - 354
121(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 831))A356 - 623
131(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 831))A625 - 831
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 / Sugars , 2 types, 4 molecules AB

#1: Protein SN243


Mass: 81872.844 Da / Num. of mol.: 2 / Mutation: D415A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Sugar ChemComp-C3G / 4-nitrophenyl beta-D-glucopyranosiduronic acid / 4-nitrophenyl beta-D-glucosiduronic acid / 4-nitrophenyl D-glucosiduronic acid / 4-nitrophenyl glucosiduronic acid


Type: D-saccharide / Mass: 315.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13NO9 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 211 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5 / 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: 2.41→85.83 Å / Num. obs: 62881 / % possible obs: 94.5 % / Redundancy: 2.1 % / CC1/2: 0.986 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.101 / Rrim(I) all: 0.16 / Net I/σ(I): 6.5 / Num. measured all: 130173 / Scaling rejects: 2080
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
2.41-2.541.90.8811732292220.4120.791.1881.894.6
7.62-85.832.30.056431118620.990.0430.07117.488.3

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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: 2.41→48.081 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 35.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2855 3061 4.97 %
Rwork0.215 58528 -
obs0.2185 61589 92.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.82 Å2 / Biso mean: 50.2063 Å2 / Biso min: 19.87 Å2
Refinement stepCycle: final / Resolution: 2.41→48.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11179 0 58 168 11405
Biso mean--92.67 44.76 -
Num. residues----1473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4472X-RAY DIFFRACTION7.59TORSIONAL
12B4472X-RAY DIFFRACTION7.59TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.41-2.44660.46111420.3812245386
2.4466-2.48670.45771330.3706249788
2.4867-2.52950.43571300.3638258088
2.5295-2.57550.47531500.3378255790
2.5755-2.62510.41721200.3217268292
2.6251-2.67860.42191170.3148266092
2.6786-2.73690.39311440.2962266393
2.7369-2.80050.35031350.2925260392
2.8005-2.87060.36341390.2866267793
2.8706-2.94820.38031440.273268293
2.9482-3.03490.38011540.2636275896
3.0349-3.13290.3091520.2395273595
3.1329-3.24480.28411290.2223273095
3.2448-3.37470.29931600.2188270095
3.3747-3.52820.30131230.2153280796
3.5282-3.71420.26271190.1915275795
3.7142-3.94680.21481480.1733268795
3.9468-4.25140.23921560.1584272295
4.2514-4.67890.19561080.147271694
4.6789-5.35510.22121840.155265794
5.3551-6.74390.24171430.193264193
6.7439-48.0810.22751310.1814256489

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