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- PDB-5k4z: M. thermoresistible IMPDH in complex with IMP and Compound 6 -

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Basic information

Entry
Database: PDB / ID: 5k4z
TitleM. thermoresistible IMPDH in complex with IMP and Compound 6
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMPDH / GuaB2 / inhibitor-complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
IMP dehydrogenase / GMP reductase 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-6Q8 / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsPacitto, A. / Ascher, D.B. / Blundell, T.L.
CitationJournal: ACS Infect Dis / Year: 2017
Title: Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis.
Authors: Park, Y. / Pacitto, A. / Bayliss, T. / Cleghorn, L.A. / Wang, Z. / Hartman, T. / Arora, K. / Ioerger, T.R. / Sacchettini, J. / Rizzi, M. / Donini, S. / Blundell, T.L. / Ascher, D.B. / Rhee, ...Authors: Park, Y. / Pacitto, A. / Bayliss, T. / Cleghorn, L.A. / Wang, Z. / Hartman, T. / Arora, K. / Ioerger, T.R. / Sacchettini, J. / Rizzi, M. / Donini, S. / Blundell, T.L. / Ascher, D.B. / Rhee, K. / Breda, A. / Zhou, N. / Dartois, V. / Jonnala, S.R. / Via, L.E. / Mizrahi, V. / Epemolu, O. / Stojanovski, L. / Simeons, F. / Osuna-Cabello, M. / Ellis, L. / MacKenzie, C.J. / Smith, A.R. / Davis, S.H. / Murugesan, D. / Buchanan, K.I. / Turner, P.A. / Huggett, M. / Zuccotto, F. / Rebollo-Lopez, M.J. / Lafuente-Monasterio, M.J. / Sanz, O. / Diaz, G.S. / Lelievre, J. / Ballell, L. / Selenski, C. / Axtman, M. / Ghidelli-Disse, S. / Pflaumer, H. / Bosche, M. / Drewes, G. / Freiberg, G.M. / Kurnick, M.D. / Srikumaran, M. / Kempf, D.J. / Green, S.R. / Ray, P.C. / Read, K. / Wyatt, P. / Barry, C.E. / Boshoff, H.I.
History
DepositionMay 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,6303
Polymers39,8541
Non-polymers7762
Water4,035224
1
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,52112
Polymers159,4184
Non-polymers3,1038
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area15450 Å2
ΔGint-93 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.270, 89.270, 84.760
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,Inosine-5'-monophosphate dehydrogenase


Mass: 39854.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Gene: RMCT_0580 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A100XBM0, UniProt: G7CNL4*PLUS, IMP dehydrogenase
#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-6Q8 / ~{N}-(4-fluorophenyl)-4-(2~{H}-indazol-6-ylsulfamoyl)-3,5-dimethyl-1~{H}-pyrrole-2-carboxamide


Mass: 427.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18FN5O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 100mM sodium acetate pH 5.5, 200mM calcium chloride, 8-14% iso-propanol

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→44.63 Å / Num. obs: 40582 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.9
Reflection shellHighest resolution: 1.64 Å / Rmerge(I) obs: 1.27

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: M. thermo IMPDH

Resolution: 1.64→44.63 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.2002 1941 4.79 %
Rwork0.1931 --
obs0.1934 40558 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 53 224 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112391
X-RAY DIFFRACTIONf_angle_d1.2133266
X-RAY DIFFRACTIONf_dihedral_angle_d13.767823
X-RAY DIFFRACTIONf_chiral_restr0.058402
X-RAY DIFFRACTIONf_plane_restr0.005419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.6810.28641660.28582724X-RAY DIFFRACTION100
1.681-1.72650.29941340.26822774X-RAY DIFFRACTION100
1.7265-1.77730.30131370.26222751X-RAY DIFFRACTION100
1.7773-1.83470.26421350.23592744X-RAY DIFFRACTION100
1.8347-1.90020.36811180.31922768X-RAY DIFFRACTION98
1.9002-1.97630.32711170.34842729X-RAY DIFFRACTION100
1.9763-2.06630.20531100.21812804X-RAY DIFFRACTION100
2.0663-2.17520.2141240.2042767X-RAY DIFFRACTION100
2.1752-2.31150.29481410.24822695X-RAY DIFFRACTION98
2.3115-2.48990.19211740.18342750X-RAY DIFFRACTION100
2.4899-2.74050.21771250.18752771X-RAY DIFFRACTION100
2.7405-3.13690.19211330.18822782X-RAY DIFFRACTION100
3.1369-3.95180.17661680.16722752X-RAY DIFFRACTION100
3.9518-44.65150.1591590.15412806X-RAY DIFFRACTION100

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