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- PDB-6rpu: Structure of the ternary complex of the IMPDH enzyme from Ashbya ... -

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Basic information

Entry
Database: PDB / ID: 6rpu
TitleStructure of the ternary complex of the IMPDH enzyme from Ashbya gossypii bound to the dinucleoside polyphosphate Ap5G and GDP
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMP dehydrogenase / Bateman domain / dinucleoside polyphosphate
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
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
ACETATE ION / P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesEremothecium gossypii ATCC 10895 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsBuey, R.M. / Fernandez-Justel, D. / Revuelta, J.L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-79237-P Spain
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The Bateman domain of IMP dehydrogenase is a binding target for dinucleoside polyphosphates.
Authors: Fernandez-Justel, D. / Pelaez, R. / Revuelta, J.L. / Buey, R.M.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1387
Polymers56,5261
Non-polymers1,6126
Water93752
1
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)465,10556
Polymers452,2118
Non-polymers12,89448
Water1448
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
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area52160 Å2
ΔGint-171 kcal/mol
Surface area126640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.538, 148.538, 103.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 56526.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eremothecium gossypii ATCC 10895 (fungus)
Gene: AGOS_AER117W / Variant: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q756Z6, IMP dehydrogenase
#2: Chemical ChemComp-G5P / P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE


Mass: 932.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O23P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Chloride, 0.1 M Sodium acetate, 20% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97725 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97725 Å / Relative weight: 1
ReflectionResolution: 2.107→85.099 Å / Num. obs: 22408 / % possible obs: 95.8 % / Redundancy: 23.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.02 / Rrim(I) all: 0.095 / Net I/σ(I): 21.5
Reflection shellResolution: 2.107→2.257 Å / Redundancy: 23.4 % / Rmerge(I) obs: 2.409 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1106 / CC1/2: 0.704 / Rpim(I) all: 0.507 / Rrim(I) all: 2.463 / % possible all: 68.4

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Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3420: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TC3

5tc3


Resolution: 2.11→85.099 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.85
RfactorNum. reflection% reflectionSelection details
Rfree0.2835 1090 4.86 %RANDOM
Rwork0.2536 ---
obs0.255 22406 66.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.11→85.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 102 53 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123414
X-RAY DIFFRACTIONf_angle_d1.1124624
X-RAY DIFFRACTIONf_dihedral_angle_d6.5172023
X-RAY DIFFRACTIONf_chiral_restr0.059535
X-RAY DIFFRACTIONf_plane_restr0.006585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1068-2.20260.4124240.3336472X-RAY DIFFRACTION12
2.2026-2.31880.3118610.32881401X-RAY DIFFRACTION35
2.3188-2.46410.3752990.32241910X-RAY DIFFRACTION48
2.4641-2.65430.33091420.32022466X-RAY DIFFRACTION62
2.6543-2.92150.36551540.31943047X-RAY DIFFRACTION76
2.9215-3.34420.32571990.30263751X-RAY DIFFRACTION94
3.3442-4.21340.26942010.24384060X-RAY DIFFRACTION100
4.2134-85.16870.24992100.21784209X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5509-0.39340.99732.2044-0.4621.5037-0.11290.6698-0.507-0.8011-0.4422-0.10820.0796-0.1976-0.61170.57240.02410.13880.6209-0.26880.3336-7.3406-22.179216.575
20.3032-0.3154-0.02120.4799-0.30610.609-0.1622-0.7908-0.06780.3484-0.3815-0.7582-0.55460.0655-0.00710.6342-0.03880.00290.63540.25450.649413.0594-33.554638.3694
30.09640.1541-0.23060.2103-0.33360.4708-0.18860.09830.12620.73270.03-0.22710.28060.7210.00020.81350.09970.1210.77010.17830.82217.3203-46.882739.5973
41.11770.46480.26590.413-0.30140.7757-0.1995-0.2960.0537-0.18350.5668-1.7443-0.43630.82550.00591.0014-0.10730.04440.9699-0.00680.957819.4081-59.00852.0619
52.9703-0.51350.68342.1367-1.02761.24380.21-0.1692-0.0582-0.3384-0.0036-0.22671.0218-0.00280.0020.9309-0.03310.10930.6436-0.00440.56398.4297-60.398543.7
60.0644-0.21270.12793.2004-1.50860.8026-0.34510.1075-0.9207-0.0068-0.0961-1.87360.2270.7466-0.36030.49670.02270.37330.5290.15351.323225.9559-33.540126.3471
71.2395-0.65960.26736.3479-3.00732.8329-0.5301-0.0857-0.4818-0.2525-0.0302-1.486-0.46460.5618-1.2660.13430.06260.58340.44240.00840.561517.8916-25.395120.1257
81.91990.56080.27871.7899-0.9780.6912-0.35370.0032-0.5834-0.07490.00650.11290.08190.13090.00070.5345-0.02870.23010.4261-0.02770.48678.2535-23.325519.1189
91.08340.4730.02192.7836-0.99540.3703-0.4799-0.7738-0.39630.6853-0.1906-0.2691-0.464-0.1186-0.51770.50330.08960.18080.72680.01360.42093.5353-26.365834.1615
103.4844-1.48430.69662.885-1.07211.9242-0.1036-0.0037-0.7021-0.0419-0.07670.378-0.1299-0.1377-0.0020.44350.01530.15210.4921-0.08430.5208-6.1373-26.214923.4477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 159 )
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 296 )
7X-RAY DIFFRACTION7chain 'A' and (resid 297 through 345 )
8X-RAY DIFFRACTION8chain 'A' and (resid 346 through 372 )
9X-RAY DIFFRACTION9chain 'A' and (resid 373 through 459 )
10X-RAY DIFFRACTION10chain 'A' and (resid 460 through 502 )

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