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- PDB-8ahf: PAC-FragmentDEL: Photoactivated covalent capture of DNA encoded f... -

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Basic information

Entry
Database: PDB / ID: 8ahf
TitlePAC-FragmentDEL: Photoactivated covalent capture of DNA encoded fragments for hit discovery
ComponentsUDP-N-acetylglucosamine 2-epimerase
KeywordsISOMERASE / INHIBITOR / COMPLEX / EPIMERASE / TECHNOLOGY
Function / homologyUDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / UDP-N-acetylglucosamine 2-epimerase activity / nucleotide binding / Chem-M3U / UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.271 Å
AuthorsBaker, L.M. / Murray, J.B. / Hubbard, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Med Chem / Year: 2022
Title: PAC-FragmentDEL - photoactivated covalent capture of DNA-encoded fragments for hit discovery.
Authors: Ma, H. / Murray, J.B. / Luo, H. / Cheng, X. / Chen, Q. / Song, C. / Duan, C. / Tan, P. / Zhang, L. / Liu, J. / Morgan, B.A. / Li, J. / Wan, J. / Baker, L.M. / Finnie, W. / Guetzoyan, L. / ...Authors: Ma, H. / Murray, J.B. / Luo, H. / Cheng, X. / Chen, Q. / Song, C. / Duan, C. / Tan, P. / Zhang, L. / Liu, J. / Morgan, B.A. / Li, J. / Wan, J. / Baker, L.M. / Finnie, W. / Guetzoyan, L. / Harris, R. / Hendrickson, N. / Matassova, N. / Simmonite, H. / Smith, J. / Hubbard, R.E. / Liu, G.
History
DepositionJul 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._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
Revision 1.2Jan 31, 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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 2-epimerase
B: UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,57112
Polymers84,1242
Non-polymers1,44710
Water4,468248
1
A: UDP-N-acetylglucosamine 2-epimerase
hetero molecules

B: UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,57112
Polymers84,1242
Non-polymers1,44710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
Buried area4360 Å2
ΔGint-134 kcal/mol
Surface area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.315, 109.315, 135.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-541-

HOH

21B-589-

HOH

31B-619-

HOH

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Components

#1: Protein UDP-N-acetylglucosamine 2-epimerase


Mass: 42062.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: GBAA_5509 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: A0A348ACF3, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)
#2: Chemical ChemComp-M3U / (2~{R},4~{S})-4-[bis(fluoranyl)methoxy]-~{N}-methyl-1-(2~{H}-pyrazolo[4,3-b]pyridin-6-ylcarbonyl)pyrrolidine-2-carboxamide


Mass: 339.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15F2N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 47.6 % / Description: Needles
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium sulfate 50 mM BIS-TRIS pH 5.6 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2021
RadiationMonochromator: Laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.271→85.17 Å / Num. obs: 36587 / % possible obs: 95.7 % / Redundancy: 26.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.201 / Net I/σ(I): 14.6
Reflection shellResolution: 2.271→2.353 Å / Redundancy: 27.7 % / Rmerge(I) obs: 3.536 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1828 / CC1/2: 0.59 / % possible all: 52.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSFeb 5, 2021data reduction
AimlessV0.7.7data scaling
REFMAC5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BEO

3beo


Resolution: 2.271→85.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.088 / SU ML: 0.169 / Cross valid method: FREE R-VALUE / ESU R: 0.322 / ESU R Free: 0.235
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2376 1828 4.996 %
Rwork0.1772 34759 -
all0.18 --
obs-36587 94.626 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.125 Å2
Baniso -1Baniso -2Baniso -3
1--0.086 Å2-0 Å2-0 Å2
2---0.086 Å2-0 Å2
3---0.172 Å2
Refinement stepCycle: LAST / Resolution: 2.271→85.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5792 0 88 248 6128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125978
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165564
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.6468108
X-RAY DIFFRACTIONr_angle_other_deg0.5591.55712986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7945736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.971044
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92101072
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.38710264
X-RAY DIFFRACTIONr_chiral_restr0.0770.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021068
X-RAY DIFFRACTIONr_nbd_refined0.2150.21210
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25210
X-RAY DIFFRACTIONr_nbtor_refined0.1620.22838
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.23207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.225
X-RAY DIFFRACTIONr_nbd_other0.1670.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.223
X-RAY DIFFRACTIONr_mcbond_it5.5334.7522950
X-RAY DIFFRACTIONr_mcbond_other5.5334.7522950
X-RAY DIFFRACTIONr_mcangle_it7.1537.1383684
X-RAY DIFFRACTIONr_mcangle_other7.1527.1383685
X-RAY DIFFRACTIONr_scbond_it7.7065.4783028
X-RAY DIFFRACTIONr_scbond_other7.455.4262997
X-RAY DIFFRACTIONr_scangle_it10.3317.9384424
X-RAY DIFFRACTIONr_scangle_other10.0057.864377
X-RAY DIFFRACTIONr_lrange_it12.47895.4225328
X-RAY DIFFRACTIONr_lrange_other12.47495.33625207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.271-2.3290.362370.2819680.28428110.9250.94235.75240.282
2.329-2.3930.3161280.26723400.26927360.9330.94790.20470.264
2.393-2.4630.2851370.23725160.2426550.9510.96199.92470.229
2.463-2.5380.2931290.21724610.22125900.9540.9691000.205
2.538-2.6210.2781210.19823800.20125010.9520.9741000.18
2.621-2.7130.3081140.19123420.19624560.9370.9751000.17
2.713-2.8160.2721160.222480.20323640.9480.9731000.177
2.816-2.9310.2381180.1721240.17422420.9640.9821000.148
2.931-3.0610.2331030.18220860.18421890.9660.9791000.159
3.061-3.210.265940.18420060.18721000.9560.9781000.16
3.21-3.3830.2371090.17618690.1819780.9650.981000.16
3.383-3.5880.2471060.18217960.18619020.9590.981000.166
3.588-3.8350.231860.16616930.16917790.9630.9841000.152
3.835-4.1420.211810.15815950.16116760.9760.9841000.15
4.142-4.5360.184700.14514800.14715500.9780.9871000.144
4.536-5.070.169630.13513430.13714060.9860.9891000.139
5.07-5.8510.257760.1711830.17512590.9750.9841000.169
5.851-7.1570.223590.17710270.1810860.9690.9821000.179
7.157-10.0860.189510.1498030.1528540.9770.9861000.17
10.086-85.170.292300.2255000.2295320.9240.95499.62410.251

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