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- PDB-6mjy: M. thermoresistible GuaB2 delta-CBS in complex with 6Cl-IMP -

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Basic information

Entry
Database: PDB / ID: 6mjy
TitleM. thermoresistible GuaB2 delta-CBS in complex with 6Cl-IMP
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Complex / Fragment / IMPDH / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE 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-type TIM barrel
Similarity search - Domain/homology
6-CHLOROPURINE RIBOSIDE, 5'-MONOPHOSPHATE / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsAscher, D.B. / Pacitto, A. / Blundell, T.L.
Funding supportEuropean Union, United Kingdom, Australia, 3items
OrganizationGrant numberCountry
European Union (EU)260872European Union
Medical Research Council (MRC, United Kingdom)MR/M026302/1 United Kingdom
National Health and Medical Research Council (NHMRC, Australia)APP1072476 Australia
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH).
Authors: Trapero, A. / Pacitto, A. / Chan, D.S. / Abell, C. / Blundell, T.L. / Ascher, D.B. / Coyne, A.G.
History
DepositionSep 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2222
Polymers39,8541
Non-polymers3681
Water4,576254
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)160,8898
Polymers159,4184
Non-polymers1,4714
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 area14250 Å2
ΔGint-91 kcal/mol
Surface area42080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.530, 88.530, 84.670
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-741-

HOH

21A-749-

HOH

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Components

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


Mass: 39854.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Gene: guaB, RMCT_0580 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A100XBM0, UniProt: G7CNL4*PLUS, IMP dehydrogenase
#2: Chemical ChemComp-CPR / 6-CHLOROPURINE RIBOSIDE, 5'-MONOPHOSPHATE


Mass: 367.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13ClN4O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
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: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→35.87 Å / Num. obs: 46334 / % possible obs: 99.8 % / Redundancy: 2 % / Net I/σ(I): 12.5
Reflection shellResolution: 1.56→1.62 Å / Mean I/σ(I) obs: 1.56

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OU1

5ou1


Resolution: 1.56→35.865 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 2299 4.96 %
Rwork0.1759 --
obs0.1767 46334 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→35.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 22 254 2447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012247
X-RAY DIFFRACTIONf_angle_d1.183073
X-RAY DIFFRACTIONf_dihedral_angle_d12.538777
X-RAY DIFFRACTIONf_chiral_restr0.051388
X-RAY DIFFRACTIONf_plane_restr0.005396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5601-1.5940.30411200.26682785X-RAY DIFFRACTION100
1.594-1.63110.26071410.25212752X-RAY DIFFRACTION100
1.6311-1.67190.25231400.25262758X-RAY DIFFRACTION100
1.6719-1.71710.31851020.23782777X-RAY DIFFRACTION100
1.7171-1.76760.23841100.23032769X-RAY DIFFRACTION100
1.7676-1.82470.23681200.20372742X-RAY DIFFRACTION100
1.8247-1.88990.26621220.2012799X-RAY DIFFRACTION100
1.8899-1.96550.19761320.19212731X-RAY DIFFRACTION100
1.9655-2.0550.23211920.18372698X-RAY DIFFRACTION100
2.055-2.16330.18941880.17112733X-RAY DIFFRACTION100
2.1633-2.29880.18641250.16612753X-RAY DIFFRACTION100
2.2988-2.47630.19521410.17372753X-RAY DIFFRACTION100
2.4763-2.72540.20841790.17862737X-RAY DIFFRACTION100
2.7254-3.11960.2021630.17852729X-RAY DIFFRACTION100
3.1196-3.92950.17161740.16062727X-RAY DIFFRACTION100
3.9295-35.8740.1441500.15072792X-RAY DIFFRACTION99

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