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- PDB-9auv: Crystal structure of A. baumannii GuaB dCBS with inhibitor GNE9123 -

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Basic information

Entry
Database: PDB / ID: 9auv
TitleCrystal structure of A. baumannii GuaB dCBS with inhibitor GNE9123
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 speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsHarris, S.F. / Wu, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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.
History
DepositionMar 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,02724
Polymers332,1798
Non-polymers5,84816
Water38,3722130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35670 Å2
ΔGint-265 kcal/mol
Surface area92740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.731, 127.277, 126.702
Angle α, β, γ (deg.)90.00, 104.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41522.379 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: guaB, HMPREF0010_03512 / Production host: Escherichia coli (E. coli) / References: UniProt: D0CF46, IMP dehydrogenase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-VOA / N-(6-chloropyridin-3-yl)-N~2~-(1,4-dihydro-2H-pyrano[3,4-c]quinolin-9-yl)-L-alaninamide


Mass: 382.843 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H19ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2130 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 20% isopropanol, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.82→97.4 Å / Num. obs: 473886 / % possible obs: 91.6 % / Redundancy: 3.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Net I/σ(I): 12.4
Reflection shellResolution: 1.82→1.92 Å / % possible obs: 77.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.517 / Num. measured all: 101082 / Num. unique obs: 30808 / CC1/2: 0.821 / Rpim(I) all: 0.337 / Rrim(I) all: 0.621 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874_finalrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→46.54 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.8 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 23912 5.05 %
Rwork0.1346 --
obs0.1373 473886 88.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19908 0 400 2141 22449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421025
X-RAY DIFFRACTIONf_angle_d0.65428503
X-RAY DIFFRACTIONf_dihedral_angle_d19.7887701
X-RAY DIFFRACTIONf_chiral_restr0.0483294
X-RAY DIFFRACTIONf_plane_restr0.0033796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.30278300.243615922X-RAY DIFFRACTION94
1.85-1.870.30147750.238415504X-RAY DIFFRACTION91
1.87-1.90.27977560.221314112X-RAY DIFFRACTION83
1.9-1.90.32521520.24793553X-RAY DIFFRACTION66
1.92-1.940.27436820.214112326X-RAY DIFFRACTION92
1.94-1.970.26959050.197316792X-RAY DIFFRACTION98
1.97-20.24758590.183416625X-RAY DIFFRACTION98
2-2.030.23198650.174616764X-RAY DIFFRACTION98
2.03-2.060.23218420.174116705X-RAY DIFFRACTION98
2.06-2.090.22295460.157410044X-RAY DIFFRACTION59
2.09-2.130.19729210.148616453X-RAY DIFFRACTION97
2.13-2.170.2158490.141916564X-RAY DIFFRACTION97
2.17-2.210.20149180.140216374X-RAY DIFFRACTION97
2.21-2.260.21985660.137211528X-RAY DIFFRACTION67
2.26-2.310.19189120.127916138X-RAY DIFFRACTION95
2.31-2.360.17838690.126315773X-RAY DIFFRACTION93
2.36-2.420.18927020.123514532X-RAY DIFFRACTION85
2.42-2.480.18958640.123616054X-RAY DIFFRACTION94
2.48-2.560.18698510.123816625X-RAY DIFFRACTION98
2.56-2.640.19359580.124316618X-RAY DIFFRACTION98
2.64-2.730.20077490.127613887X-RAY DIFFRACTION82
2.73-2.840.19188520.128116617X-RAY DIFFRACTION97
2.84-2.970.21138820.133316490X-RAY DIFFRACTION97
2.97-3.130.17948580.126316523X-RAY DIFFRACTION97
3.13-3.320.17468280.128715945X-RAY DIFFRACTION94
3.33-3.580.17527780.121714681X-RAY DIFFRACTION87
3.58-3.940.15946970.119213441X-RAY DIFFRACTION79
3.94-4.510.14288980.102816044X-RAY DIFFRACTION95
4.51-5.680.15249340.116315859X-RAY DIFFRACTION94
5.68-46.540.16098140.143115481X-RAY DIFFRACTION91

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