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- PDB-3khj: C. parvum inosine monophosphate dehydrogenase bound by inhibitor C64 -

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Basic information

Entry
Database: PDB / ID: 3khj
TitleC. parvum inosine monophosphate dehydrogenase bound by inhibitor C64
ComponentsInosine-5-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / enzyme-inhibitor complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / 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 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-C64 / INOSINIC ACID / Inosine-5-monophosphate dehydrogenase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMacPherson, I.S. / Hedstrom, L.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: The structural basis of Cryptosporidium -specific IMP dehydrogenase inhibitor selectivity.
Authors: Macpherson, I.S. / Kirubakaran, S. / Gorla, S.K. / Riera, T.V. / D'Aquino, J.A. / Zhang, M. / Cuny, G.D. / Hedstrom, L.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 2, 2014Group: Structure summary
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: Inosine-5-monophosphate dehydrogenase
F: Inosine-5-monophosphate dehydrogenase
G: Inosine-5-monophosphate dehydrogenase
H: Inosine-5-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,21620
Polymers308,1328
Non-polymers4,08512
Water3,747208
1
A: Inosine-5-monophosphate dehydrogenase
B: Inosine-5-monophosphate dehydrogenase
C: Inosine-5-monophosphate dehydrogenase
D: Inosine-5-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,34411
Polymers154,0664
Non-polymers2,2787
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13870 Å2
ΔGint-92 kcal/mol
Surface area44790 Å2
MethodPISA
2
E: Inosine-5-monophosphate dehydrogenase
F: Inosine-5-monophosphate dehydrogenase
G: Inosine-5-monophosphate dehydrogenase
H: Inosine-5-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8729
Polymers154,0664
Non-polymers1,8065
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-88 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.481, 166.141, 101.289
Angle α, β, γ (deg.)90.00, 105.14, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTetramer

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Components

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


Mass: 38516.441 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa-II / Gene: cgd6_20, GuaB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q5CPK7, IMP dehydrogenase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-C64 / N-(4-bromophenyl)-2-[2-(1,3-thiazol-2-yl)-1H-benzimidazol-1-yl]acetamide


Mass: 413.291 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H13BrN4OS
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 295 K / Method: microbatch under oil / pH: 4.6
Details: 30% MPD, 100 mM sodium acetate pH 4.6, 20 mM calcium chloride, microbatch under oil, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9194 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. all: 65589 / Num. obs: 65589 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREP(CCP4)phasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→42.135 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.885 / SU B: 16.103 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26627 3303 5.1 %RANDOM
Rwork0.22427 ---
obs0.22643 61921 99.13 %-
all-65589 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.214 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å20.04 Å2
2---0.42 Å20 Å2
3---4.06 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18009 0 263 208 18480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02218502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9982.00625004
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.37352461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89525.338577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.139153347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.641571
X-RAY DIFFRACTIONr_chiral_restr0.0570.23039
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1610.29044
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2870.212933
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2720
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0340.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2071.512472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.371219427
X-RAY DIFFRACTIONr_scbond_it0.30536818
X-RAY DIFFRACTIONr_scangle_it0.5564.55574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.796→2.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 238 -
Rwork0.288 4374 -
obs--94.57 %

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