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- PDB-7qee: SN243 mutant D415N bound to para-nitrophenyl-Beta-D-glucuronide -

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Basic information

Entry
Database: PDB / ID: 7qee
TitleSN243 mutant D415N bound to para-nitrophenyl-Beta-D-glucuronide
ComponentsSN243
KeywordsHYDROLASE / enzyme discovery / carbohydrate-active enzymes (CAZy) / protein engineering / functional metagenomics)
Function / homologybeta-D-glucopyranuronic acid / 4-nitrophenyl beta-D-glucopyranosiduronic acid
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.374 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 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: SN243
B: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,61836
Polymers163,8322
Non-polymers2,78634
Water1,820101
1
A: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,40018
Polymers81,9161
Non-polymers1,48417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,21818
Polymers81,9161
Non-polymers1,30217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.499, 82.173, 93.041
Angle α, β, γ (deg.)113.690, 90.650, 90.310
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))
21(chain B and (resid 40 through 202 or resid 204...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPHEPHE(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 785))AA40 - 35410 - 324
12ALAALAGLYGLY(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 785))AA356 - 623326 - 593
13SERSERASPASP(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 785))AA625 - 785595 - 755
21GLUGLUALAALA(chain B and (resid 40 through 202 or resid 204...BB40 - 20210 - 172
22GLYGLYPHEPHE(chain B and (resid 40 through 202 or resid 204...BB204 - 354174 - 324
23ALAALAGLYGLY(chain B and (resid 40 through 202 or resid 204...BB356 - 623326 - 593
24SERSERASPASP(chain B and (resid 40 through 202 or resid 204...BB625 - 785595 - 755

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SN243


Mass: 81915.867 Da / Num. of mol.: 2 / Mutation: D415N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic construct (others) / Plasmid: pSol / Production host: Escherichia coli BL21 (bacteria)

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Sugars , 2 types, 2 molecules

#4: 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.: 1 / Source method: isolated from a natural source / Formula: C12H13NO9 / Feature type: SUBJECT OF INVESTIGATION
#5: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 133 molecules

#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


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
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: 2.37→75.24 Å / Num. obs: 65955 / % possible obs: 96.3 % / Redundancy: 2.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.092 / Rrim(I) all: 0.165 / Net I/σ(I): 2.5 / Num. measured all: 181699 / Scaling rejects: 94
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
2.37-2.51.60.7621444192490.4570.7621.0780.792.3
7.51-75.243.10.065651020780.990.0420.0774.996.1

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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: 2.374→47.819 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2729 3410 5.2 %
Rwork0.2168 62123 -
obs0.2197 65533 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 905.64 Å2 / Biso mean: 57.966 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.374→47.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11229 0 56 101 11386
Biso mean--96.42 61.23 -
Num. residues----1478
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4440X-RAY DIFFRACTION6.389TORSIONAL
12B4440X-RAY DIFFRACTION6.389TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3742-2.40810.36511110.3741246388
2.4081-2.44410.39461120.3764237288
2.4441-2.48230.38591330.3652245291
2.4823-2.5230.41141100.3605248591
2.523-2.56650.37441160.3461249692
2.5665-2.61310.38731570.3365258695
2.6131-2.66340.38621570.3325257697
2.6634-2.71770.37071620.3058263597
2.7177-2.77680.34571430.2848257798
2.7768-2.84140.31471790.2716266798
2.8414-2.91250.31441240.2662262898
2.9125-2.99120.33871250.2463268098
2.9912-3.07920.32181250.2547263397
3.0792-3.17860.31511260.239264997
3.1786-3.29220.27241480.2357266298
3.2922-3.42390.27591500.2121264298
3.4239-3.57970.31111550.2055262098
3.5797-3.76840.26081630.1972258497
3.7684-4.00440.23261290.1689268598
4.0044-4.31340.24881250.159263397
4.3134-4.74710.21471600.1447260397
4.7471-5.43320.20751780.159259997
5.4332-6.8420.24081810.1928260897
6.842-47.8190.23191410.1927258896

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