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- PDB-4rv8: Co-Crystal Structure of the Catalytic Domain of the Inosine Monop... -

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Basic information

Entry
Database: PDB / ID: 4rv8
TitleCo-Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Cryptosporidium parvum and the inhibitor p131
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold / TIM barrel
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / 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 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-I13 / INOSINIC ACID / DI(HYDROXYETHYL)ETHER / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Kavitha, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structure of Cryptosporidium IMP dehydrogenase bound to an inhibitor with in vivo antiparasitic activity.
Authors: Kim, Y. / Makowska-Grzyska, M. / Gorla, S.K. / Gollapalli, D.R. / Cuny, G.D. / Joachimiak, A. / Hedstrom, L.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Feb 8, 2017Group: Structure summary
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,92718
Polymers154,2184
Non-polymers3,70914
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20040 Å2
ΔGint-115 kcal/mol
Surface area46230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.188, 91.832, 92.021
Angle α, β, γ (deg.)90.00, 103.75, 90.00
Int Tables number4
Space group name H-MP1211
Detailsone tetramer in the asymmetric unit

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 38554.422 Da / Num. of mol.: 4 / Fragment: Catalytic domain of IMPDH / Mutation: delta 93-134, 90-92 are mutated to SGG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: 56k.02, cgd6_20 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q8T6T2, IMP dehydrogenase

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Non-polymers , 5 types, 353 molecules

#2: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-I13 / 1-(2-{3-[(1E)-N-(2-aminoethoxy)ethanimidoyl]phenyl}propan-2-yl)-3-(4-chloro-3-nitrophenyl)urea


Mass: 433.889 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24ClN5O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bicine pH 9.0, 20%(w/v) PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 16K, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 89862 / Num. obs: 89862 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 27.54 Å2 / Rsym value: 0.14 / Net I/σ(I): 12.66
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.02 / Num. unique all: 4514 / Rsym value: 0.695 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FFS

3ffs


Resolution: 2.053→40.842 Å / SU ML: 0.24 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4499 5.01 %RANDOM
Rwork0.187 ---
all0.189 89795 --
obs0.189 89795 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.1 Å2
Refinement stepCycle: LAST / Resolution: 2.053→40.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9650 0 250 339 10239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410188
X-RAY DIFFRACTIONf_angle_d0.86413746
X-RAY DIFFRACTIONf_dihedral_angle_d12.0663862
X-RAY DIFFRACTIONf_chiral_restr0.0311623
X-RAY DIFFRACTIONf_plane_restr0.0031718
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0526-2.07590.33091390.27752661280093
2.0759-2.10040.30891530.256828352988100
2.1004-2.1260.30541400.254228743014100
2.126-2.15290.3151360.233227962932100
2.1529-2.18120.29621710.230928132984100
2.1812-2.21110.25781650.22528132978100
2.2111-2.24270.28691680.211328683036100
2.2427-2.27620.25241430.213728162959100
2.2762-2.31170.25431320.195828652997100
2.3117-2.34960.27751480.198928452993100
2.3496-2.39010.26461350.199828382973100
2.3901-2.43360.24511460.196128512997100
2.4336-2.48040.22271760.189428263002100
2.4804-2.5310.24811470.185428452992100
2.531-2.5860.23341550.199128412996100
2.586-2.64620.25841320.185728672999100
2.6462-2.71230.24831480.192328653013100
2.7123-2.78570.24971540.182928693023100
2.7857-2.86760.25031540.189128092963100
2.8676-2.96010.24111370.189128743011100
2.9601-3.06590.23971500.191228462996100
3.0659-3.18860.23191510.186128533004100
3.1886-3.33370.22361710.191628112982100
3.3337-3.50930.21571450.179228633008100
3.5093-3.72910.21541520.177228793031100
3.7291-4.01680.2141490.158428623011100
4.0168-4.42050.17151520.150828603012100
4.4205-5.05920.1831640.146928593023100
5.0592-6.37020.21091620.191628783040100
6.3702-40.85050.21051240.19712914303898
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)
10.8666-0.62641.01358.0906-4.54243.1458-0.082-0.0020.08480.71160.0855-0.0154-0.2701-0.0048-0.00260.1954-0.010.08340.1573-0.01770.1386-12.414810.262896.6696
23.17770.7624-0.93381.7307-0.07262.8441-0.03210.2051-0.3074-0.03620.036-0.18550.23620.19410.00370.29080.03990.04350.1991-0.06340.19034.534-0.333780.5478
34.6081-2.3474-0.79752.80920.96513.18690.12490.5059-0.0932-0.4934-0.0786-0.12520.14140.2564-0.04930.4057-0.00810.04820.3121-0.02490.18621.18069.188268.5385
40.9946-0.1117-0.72123.1668-0.79730.67770.0010.0888-0.1005-0.0073-0.0518-0.0388-0.00490.0360.05360.24330.01020.0310.1739-0.02780.1482-5.144211.823385.3208
54.9142-3.59791.58255.9837-0.21723.27520.02750.14120.5004-0.0804-0.0838-0.44860.08110.6260.09630.2333-0.01360.05520.3339-0.04530.283416.740513.380787.2675
65.0852-0.36570.72151.4448-0.88812.11140.22060.0557-0.20050.014-0.1041-0.14320.2103-0.0267-0.1080.30910.00480.0320.1021-0.00020.1733-4.2507-0.047296.754
71.61940.0435-0.4293.10472.95863.76380.0946-0.029-0.007-0.1716-0.00790.0371-0.6190.1635-0.0420.2830.0320.02590.11020.0080.1921-17.157415.0895115.9399
82.2727-1.3059-0.2553.27860.01381.15040.0387-0.1879-0.2520.2317-0.0377-0.01140.0938-0.0040.00870.4193-0.03580.00160.21680.0630.2157-7.699-4.6809129.1517
92.7473-0.7031.70083.2193-1.50793.44870.1599-0.1214-0.53790.2074-0.0823-0.07270.3692-0.026-0.07690.3826-0.0273-0.01130.16770.03980.337-11.1501-15.4937118.3505
100.6137-0.6561-0.26660.76990.63381.77040.1042-0.067-0.14030.0611-0.0213-0.0136-0.0889-0.0208-0.09490.3664-0.02960.01070.20140.01570.2182-12.57752.3061115.4097
113.60911.17273.5942.76391.13017.29180.25260.1705-0.21750.09340.0197-0.50110.08140.5803-0.24830.33310.0092-0.01860.24340.06190.31788.9404-1.0823119.3369
124.0854-0.60351.63012.19320.632.5420.1353-0.297-0.09920.0849-0.0704-0.1243-0.0171-0.0283-0.05930.3154-0.01640.03570.16240.01270.1203-11.794212.8715127.8405
131.3160.84110.26951.3953-0.57212.11490.0428-0.16220.13970.1603-0.06120.0578-0.4014-0.14910.04530.25920.04940.02860.1986-0.01960.1603-15.236542.1171118.8319
142.3373-0.04340.01451.4181-0.17994.4832-0.0739-0.48320.1350.48340.0242-0.26780.07180.05390.08660.42260.0044-0.01180.3295-0.03930.1809-4.147341.3518142.0739
153.66251.19051.32012.37651.82124.4302-0.0464-0.42740.12660.40750.05910.1530.0043-0.1520.010.47760.00220.0820.3206-0.02270.1884-19.107134.5867141.3151
160.22320.51340.03952.1349-0.39550.2221-0.0466-0.18870.00790.0097-0.0035-0.03690.002-0.04150.04590.37950.00490.02220.2492-0.02050.1601-14.762233.1979124.7443
173.01590.88230.55752.35970.18162.31410.0847-0.2967-0.14790.1110.0689-0.50050.1940.3813-0.11150.38740.0341-0.00620.3558-0.07280.23045.75332.1302132.7402
182.75040.09610.88491.8552-0.00232.19330.09-0.04040.27290.0842-0.09010.0051-0.11650.04520.02450.3363-0.00820.02230.1703-0.00940.1695-8.64345.0665115.0016
193.0708-2.183-2.23743.38963.16864.2738-0.2012-0.1049-0.03530.195-0.00910.14660.5602-0.04660.19670.2464-0.05050.00890.10970.00550.1823-11.229230.067692.0498
202.16930.85160.4432.85741.28122.3609-0.05380.15340.2051-0.15870.0035-0.0944-0.1910.10370.07320.2918-0.02420.02880.17750.05840.21173.515449.583984.6419
214.64291.1991-0.70372.9505-0.5871.51990.07510.10270.59310.0223-0.0964-0.1215-0.36610.0607-0.01160.38660.0091-0.00720.15730.02940.3056-4.600560.552492.7219
220.79440.1638-0.3270.62850.85721.5759-0.10190.00690.12870.1880.02320.01890.02970.01670.0740.27770.00010.01330.16350.01980.2169-7.345842.775394.5864
236.0244-0.646-3.1212.29880.19465.28720.0805-0.53090.22930.1473-0.0489-0.5241-0.18840.5866-0.11970.2288-0.0488-0.03180.21880.03630.306213.353246.0373101.4177
244.7374-0.12630.86542.19120.67941.62070.05570.29250.1073-0.1988-0.0338-0.0628-0.0170.1238-0.02010.302-0.02250.06450.1362-0.01640.135-1.000131.888483.9231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 203 )
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 274 )
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 340 )
6X-RAY DIFFRACTION6chain 'A' and (resid 341 through 392 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 25 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 76 )
9X-RAY DIFFRACTION9chain 'B' and (resid 77 through 203 )
10X-RAY DIFFRACTION10chain 'B' and (resid 204 through 274 )
11X-RAY DIFFRACTION11chain 'B' and (resid 275 through 340 )
12X-RAY DIFFRACTION12chain 'B' and (resid 341 through 392 )
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 47 )
14X-RAY DIFFRACTION14chain 'C' and (resid 48 through 88 )
15X-RAY DIFFRACTION15chain 'C' and (resid 89 through 203 )
16X-RAY DIFFRACTION16chain 'C' and (resid 204 through 274 )
17X-RAY DIFFRACTION17chain 'C' and (resid 275 through 340 )
18X-RAY DIFFRACTION18chain 'C' and (resid 341 through 392 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 25 )
20X-RAY DIFFRACTION20chain 'D' and (resid 26 through 76 )
21X-RAY DIFFRACTION21chain 'D' and (resid 77 through 203 )
22X-RAY DIFFRACTION22chain 'D' and (resid 204 through 274 )
23X-RAY DIFFRACTION23chain 'D' and (resid 275 through 340 )
24X-RAY DIFFRACTION24chain 'D' and (resid 341 through 392 )

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