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- PDB-9av0: Crystal structure of S. aureus GuaB dCBS with inhibitor GNE2011 -

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Basic information

Entry
Database: PDB / ID: 9av0
TitleCrystal structure of S. aureus GuaB dCBS with inhibitor GNE2011
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GuaB / inhibitor
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHarris, S.F. / Wu, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Mbio / Year: 2024
Title: Discovery of GuaB inhibitors with efficacy against Acinetobacter baumannii infection.
Authors: Kofoed, E.M. / Aliagas, I. / Crawford, T. / Mao, J. / Harris, S.F. / Xu, M. / Wang, S. / Wu, P. / Ma, F. / Clark, K. / Sims, J. / Xu, Y. / Peng, Y. / Skippington, E. / Yang, Y. / Reeder, J. ...Authors: Kofoed, E.M. / Aliagas, I. / Crawford, T. / Mao, J. / Harris, S.F. / Xu, M. / Wang, S. / Wu, P. / Ma, F. / Clark, K. / Sims, J. / Xu, Y. / Peng, Y. / Skippington, E. / Yang, Y. / Reeder, J. / Ubhayakar, S. / Baumgardner, M. / Yan, Z. / Chen, J. / Park, S. / Zhang, H. / Yen, C.-W. / Lorenzo, M. / Skelton, N. / Liang, X. / Chen, L. / Hoag, B. / Li, C.S. / Liu, Z. / Wai, J. / Liu, X. / Liang, J. / Tan, M.W.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2024
Title: Discovery of potent dihydro-oxazinoquinolinone inhibitors of GuaB for the treatment of tuberculosis.
Authors: Zhou, Y. / Aliagas, I. / Wang, S. / Li, C.S. / Liu, Z. / Bowman, C.M. / Burdick, D.J. / Clark, K.R. / Dening, T.J. / Flygare, J. / Ganti, A. / Girgis, H.S. / Hanan, E.J. / Harris, S.F. / Hu, ...Authors: Zhou, Y. / Aliagas, I. / Wang, S. / Li, C.S. / Liu, Z. / Bowman, C.M. / Burdick, D.J. / Clark, K.R. / Dening, T.J. / Flygare, J. / Ganti, A. / Girgis, H.S. / Hanan, E.J. / Harris, S.F. / Hu, C. / Kapadia, S.B. / Koehler, M.F.T. / Lai, T. / Liang, J. / Liu, X. / Ma, F. / Mao, J. / Nicolai, J. / Sims, J. / Unhayaker, S. / Wai, J. / Wang, X. / Wu, P. / Xu, Y. / Yen, C.W. / Zhang, R. / Elfert, T.F. / Tan, M.W. / Kofoed, E.M. / Crawford, T.D.
History
DepositionMar 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3533
Polymers40,5981
Non-polymers7552
Water52229
1
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,41312
Polymers162,3934
Non-polymers3,0208
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area16290 Å2
ΔGint-88 kcal/mol
Surface area46950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.442, 104.442, 64.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


Mass: 40598.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: guaB, SAUSA300_0388 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FJM6, IMP dehydrogenase
#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-A1AG0 / 9-{(1R)-1-[(5P)-5-(4-chloro-1H-imidazol-2-yl)pyridin-3-yl]ethoxy}-1,4-dihydro-2H-pyrano[3,4-c]quinoline


Mass: 406.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M Bicine pH 9, 0.1M NaCl, 30% PEG550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→73.85 Å / Num. obs: 17517 / % possible obs: 98.4 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Net I/σ(I): 16.6 / Num. measured all: 115512
Reflection shellResolution: 2.2→2.32 Å / % possible obs: 90.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.862 / Num. measured all: 15795 / Num. unique obs: 2351 / CC1/2: 0.719 / Rpim(I) all: 0.357 / Rrim(I) all: 0.934 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→73.85 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.928 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.302 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.287 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.214
RfactorNum. reflection% reflectionSelection details
Rfree0.251 905 5.19 %RANDOM
Rwork0.225 ---
obs0.226 17437 98.3 %-
Displacement parametersBiso mean: 76.29 Å2
Baniso -1Baniso -2Baniso -3
1-6.0511 Å20 Å20 Å2
2--6.0511 Å20 Å2
3----12.1021 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.2→73.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 52 29 2480
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082632HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.083588HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d936SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes411HARMONIC5
X-RAY DIFFRACTIONt_it2632HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion19.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion349SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3111SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.28 128 4.91 %
Rwork0.251 2479 -
all0.252 2607 -
obs--91.52 %

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