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- PDB-9av2: Crystal structure of E. coli GuaB dCBS with inhibitor GNE9979 -

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Basic information

Entry
Database: PDB / ID: 9av2
TitleCrystal structure of E. coli 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6503
Polymers39,9031
Non-polymers7472
Water3,783210
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)162,60112
Polymers159,6134
Non-polymers2,9888
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15470 Å2
ΔGint-98 kcal/mol
Surface area45550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.343, 113.343, 54.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-1109-

HOH

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Components

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


Mass: 39903.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: guaB, Z3772, ECs3370 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADG8, 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-VP4 / N-[4-chloro-3-(dimethylamino)phenyl]-N~2~-[3-(hydroxymethyl)quinolin-6-yl]-L-alaninamide


Mass: 398.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine pH 9, 20% PEG6000

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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: 1.7→56.67 Å / Num. obs: 37545 / % possible obs: 97.3 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.076 / Net I/σ(I): 12.7 / Num. measured all: 242199
Reflection shellResolution: 1.7→1.79 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.797 / Num. measured all: 37647 / Num. unique obs: 5586 / CC1/2: 0.843 / Rpim(I) all: 0.331 / Rrim(I) all: 0.864 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1883 5.03 %RANDOM
Rwork0.204 ---
obs0.206 37419 97.2 %-
Displacement parametersBiso mean: 40.54 Å2
Baniso -1Baniso -2Baniso -3
1-5.9338 Å20 Å20 Å2
2--5.9338 Å20 Å2
3----11.8676 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.7→24.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 51 210 2627
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012489HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.143374HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d886SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes392HARMONIC5
X-RAY DIFFRACTIONt_it2489HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion17.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion336SEMIHARMONIC5
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_contact3215SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.75 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.304 172 5.74 %
Rwork0.271 2824 -
all0.273 2996 -
obs--99.9 %

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