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

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Basic information

Entry
Database: PDB / ID: 8ahe
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 activity / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / nucleotide binding / ~{N},5-dimethyl-1-phenyl-pyrazole-4-sulfonamide / UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.108 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)85,20310
Polymers84,1242
Non-polymers1,0798
Water4,125229
1
A: UDP-N-acetylglucosamine 2-epimerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)85,20310
Polymers84,1242
Non-polymers1,0798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
Buried area3970 Å2
ΔGint-107 kcal/mol
Surface area30550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.119, 109.119, 136.207
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-518-

HOH

21B-594-

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-M2U / ~{N},5-dimethyl-1-phenyl-pyrazole-4-sulfonamide


Mass: 251.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.38 Å3/Da / Density % sol: 48.02 % / 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: 2.108→85.161 Å / Num. obs: 39374 / % possible obs: 95.6 % / Redundancy: 26.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.216 / Net I/σ(I): 13.7
Reflection shellResolution: 2.108→2.285 Å / Redundancy: 25.5 % / Rmerge(I) obs: 2.657 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1970 / CC1/2: 0.582 / % possible all: 58.7

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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: 2.108→85.161 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.143 / SU ML: 0.174 / Cross valid method: FREE R-VALUE / ESU R: 0.288 / ESU R Free: 0.217
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2347 1989 5.052 %
Rwork0.1844 37385 -
all0.187 --
obs-39374 81.906 %
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: 44.579 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å20 Å20 Å2
2--0.005 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.108→85.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5779 0 64 229 6072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125941
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165546
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.6458058
X-RAY DIFFRACTIONr_angle_other_deg0.5611.55612931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.3281039
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.356101064
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.42910261
X-RAY DIFFRACTIONr_chiral_restr0.0810.2940
X-RAY DIFFRACTIONr_chiral_restr_other0.0890.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021067
X-RAY DIFFRACTIONr_nbd_refined0.2140.21180
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25234
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22829
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23155
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.224
X-RAY DIFFRACTIONr_nbd_other0.1830.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.222
X-RAY DIFFRACTIONr_mcbond_it5.1084.3972950
X-RAY DIFFRACTIONr_mcbond_other5.1084.3972950
X-RAY DIFFRACTIONr_mcangle_it6.6146.63684
X-RAY DIFFRACTIONr_mcangle_other6.6146.63685
X-RAY DIFFRACTIONr_scbond_it7.1925.0752991
X-RAY DIFFRACTIONr_scbond_other7.0265.0462968
X-RAY DIFFRACTIONr_scangle_it9.7277.3394374
X-RAY DIFFRACTIONr_scangle_other9.5057.2944339
X-RAY DIFFRACTIONr_lrange_it11.79188.08625111
X-RAY DIFFRACTIONr_lrange_other11.77488.1125002
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
2.108-2.1630.404140.3312280.33634980.9140.8916.91820.326
2.163-2.2220.272270.2615370.26133930.9560.9416.62250.259
2.222-2.2870.341650.27911340.28333250.9050.94336.06020.278
2.287-2.3570.3061380.27826040.2832160.9370.94685.26120.274
2.357-2.4340.2871460.24729820.24931280.9410.9611000.238
2.434-2.5190.2851530.22328890.22630420.9450.9681000.207
2.519-2.6140.2681440.20727870.21129310.9560.9711000.189
2.614-2.7210.2411310.19426810.19628120.9580.9741000.173
2.721-2.8420.2691370.19525720.19927090.9520.9751000.171
2.842-2.9810.2541340.1924680.19326020.9570.9761000.164
2.981-3.1420.251360.19223410.19524770.9570.9761000.168
3.142-3.3320.2741030.18522650.18823680.9540.981000.168
3.332-3.5610.2341100.18320950.18522050.9660.9811000.168
3.561-3.8460.2231160.17919510.18120670.970.9831000.165
3.846-4.2130.2041120.15918180.16119300.9740.9851000.149
4.213-4.7080.191790.13716650.13917440.9720.9891000.133
4.708-5.4340.191900.15314730.15515630.980.9871000.147
5.434-6.6480.249680.19912700.20113380.9670.9781000.186
6.648-9.3740.196540.16210100.16310640.980.9841000.167
9.374-85.1610.228320.2016150.2026480.9670.96399.84570.215

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