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- PDB-7qg4: Apo crystal structure of a mutant of SN243 (D415N) -

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Basic information

Entry
Database: PDB / ID: 7qg4
TitleApo crystal structure of a mutant of SN243 (D415N)
ComponentsSN243
KeywordsHYDROLASE / enzyme discovery / carbohydrate-active enzymes (CAZy) / protein engineering / functional metagenomics)
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 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 7, 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)165,62829
Polymers163,8322
Non-polymers1,79727
Water7,098394
1
A: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,92816
Polymers81,9161
Non-polymers1,01215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,70113
Polymers81,9161
Non-polymers78512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.396, 82.413, 92.077
Angle α, β, γ (deg.)113.330, 90.430, 90.940
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SN243


Mass: 81915.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 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: 2.08→75.98 Å / Num. obs: 100349 / % possible obs: 97.8 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Rrim(I) all: 0.131 / Net I/σ(I): 5.3 / Num. measured all: 347587 / Scaling rejects: 21
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
2.08-2.193.51.99151390145790.4041.2482.3530.697
6.57-75.983.40.0551082632040.9940.0350.06517.798.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QE1

7qe1


Resolution: 2.08→75.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.007 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 4934 5.1 %RANDOM
Rwork0.2488 ---
obs0.2489 91984 91.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.64 Å2 / Biso mean: 42.924 Å2 / Biso min: 13.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å20.1 Å2-1.43 Å2
2--4.48 Å2-3.23 Å2
3---0.75 Å2
Refinement stepCycle: final / Resolution: 2.08→75.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11346 0 31 394 11771
Biso mean--73.27 39.24 -
Num. residues----1492
LS refinement shellResolution: 2.08→2.102 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.64 254 -
Rwork0.593 4201 -
obs--56.84 %

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