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- PDB-6kcf: Structure of Inosine 5'-monophosphate Dehydrogenase from Candidat... -

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Basic information

Entry
Database: PDB / ID: 6kcf
TitleStructure of Inosine 5'-monophosphate Dehydrogenase from Candidatus Liberibacter asiaticus str. psy62
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Inosine 5'-monophosphate Dehydrogenase
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP 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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesLiberibacter asiaticus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsNan, J. / Zhang, S.R. / Jiang, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31572099 China
National Natural Science Foundation of China31872064 China
CitationJournal: Molecules / Year: 2020
Title: Evaluation of Bronopol and Disulfiram as Potential Candidatus Liberibacter asiaticus Inosine 5'-Monophosphate Dehydrogenase Inhibitors by Using Molecular Docking and Enzyme Kinetic.
Authors: Nan, J. / Zhang, S. / Zhan, P. / Jiang, L.
History
DepositionJun 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)164,2404
Polymers164,2404
Non-polymers00
Water75742
1
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase

C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)164,2404
Polymers164,2404
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9170 Å2
ΔGint-64 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.126, 134.857, 85.617
Angle α, β, γ (deg.)90.000, 101.210, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 41059.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Liberibacter asiaticus (strain psy62) (bacteria)
Strain: psy62 / Gene: quaB, guaB, CLIBASIA_03930 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6XG59, IMP dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG 400, 100 mM HEPES pH 7.5, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.55→42.469 Å / Num. obs: 51023 / % possible obs: 98.2 % / Redundancy: 2.58 % / Net I/σ(I): 19.9
Reflection shellResolution: 2.55→3 Å / Num. unique obs: 50928

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→42.469 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.72
RfactorNum. reflection% reflection
Rfree0.2645 2539 4.99 %
Rwork0.2223 --
obs0.2244 50928 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.3 Å2 / Biso mean: 69.2922 Å2 / Biso min: 29.05 Å2
Refinement stepCycle: final / Resolution: 2.55→42.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8256 0 0 42 8298
Biso mean---60.31 -
Num. residues----1135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.5990.34371740.2167267698
2.599-2.65210.3251370.229273299
2.6521-2.70970.36461500.2167263898
2.7097-2.77280.31411480.2167267699
2.7728-2.84210.31411350.2167267798
2.8421-2.91890.30151090.2167255092
2.9189-3.00480.29111340.2167271099
3.0048-3.10170.29811330.2167271699
3.1017-3.21260.28651750.21672684100
3.2126-3.34110.30151540.2167270499
3.3411-3.49310.29031370.2167273199
3.4931-3.67720.27751470.2167271799
3.6772-3.90750.2671290.2167273199
3.9075-4.20890.26891340.1961259094
4.2089-4.6320.21671430.1919269198
4.632-5.30120.22981340.19252731100
5.3012-6.67470.24911420.2167274799
6.6747-42.4690.2291240.2058268895

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