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- PDB-9auw: Crystal structure of A. baumannii GuaB dCBS with inhibitor GNE9979 -

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Basic information

Entry
Database: PDB / ID: 9auw
TitleCrystal structure of A. baumannii GuaB dCBS with inhibitor GNE9979
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 / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)338,15624
Polymers332,1798
Non-polymers5,97716
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35870 Å2
ΔGint-275 kcal/mol
Surface area90230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.720, 127.299, 127.478
Angle α, β, γ (deg.)90.00, 101.82, 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, guaB, guaB_1, guaB_2 / Production host: Escherichia coli (E. coli)
References: UniProt: P31002, UniProt: A0A059ZJE9, 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-VP4 / N-[4-chloro-3-(dimethylamino)phenyl]-N~2~-[3-(hydroxymethyl)quinolin-6-yl]-L-alaninamide


Mass: 398.886 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H23ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
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: 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: 2.29→124.77 Å / Num. obs: 157659 / % possible obs: 99.1 % / Redundancy: 6.1 % / CC1/2: 0.936 / Rmerge(I) obs: 0.409 / Rpim(I) all: 0.177 / Rrim(I) all: 0.447 / Net I/σ(I): 2.6 / Num. measured all: 958600
Reflection shellResolution: 2.29→2.42 Å / % possible obs: 98.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.679 / Num. measured all: 88270 / Num. unique obs: 22791 / CC1/2: 0.803 / Rpim(I) all: 0.378 / Rrim(I) all: 0.782 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46 Å / Cor.coef. Fo:Fc: 0.804 / Cor.coef. Fo:Fc free: 0.78 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.284 / SU Rfree Blow DPI: 0.215 / SU Rfree Cruickshank DPI: 0.222
RfactorNum. reflection% reflectionSelection details
Rfree0.265 7965 5.1 %RANDOM
Rwork0.244 ---
obs0.245 156055 99 %-
Displacement parametersBiso mean: 28.15 Å2
Baniso -1Baniso -2Baniso -3
1--15.7624 Å20 Å2-5.7564 Å2
2--8.3079 Å20 Å2
3---7.4546 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: 1 / Resolution: 2.3→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19566 0 408 445 20419
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00920603HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1128003HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7115SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes410HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3203HARMONIC5
X-RAY DIFFRACTIONt_it20603HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion18.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2758SEMIHARMONIC5
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_contact24320SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 579 5.11 %
Rwork0.211 10748 -
all0.212 11327 -
obs--97.15 %

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