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- PDB-4qj1: Co-crystal structure of the catalytic domain of the inosine monop... -

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Basic information

Entry
Database: PDB / ID: 4qj1
TitleCo-crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from Cryptosporidium parvum with inhibitor N109
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold / TIM barrel / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP 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
ACETIC ACID / FORMIC ACID / INOSINIC ACID / Chem-N09 / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.415 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Co-crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from Cryptosporidium parvum with inhibitor N109
Authors: Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Sep 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,24617
Polymers154,0264
Non-polymers3,22013
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24050 Å2
ΔGint-108 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.412, 92.337, 91.914
Angle α, β, γ (deg.)90.00, 104.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 38506.426 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 / 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 , 6 types, 146 molecules

#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-N09 / N-(4-chloro-3-methoxyphenyl)-2-(4-oxochromeno[4,3-c]pyrazol-1(4H)-yl)acetamide


Mass: 383.785 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H14ClN3O4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsUNP RESIDUES 90-131 ARE DELETED.

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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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 289 K / pH: 7
Details: 0.1 M HEPES, pH 7.0, 5% v/v Tacsimate, pH 7.0, 10% w/v PEG5000 MME, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2014 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 55500 / Num. obs: 55500 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 35.9 Å2 / Rsym value: 0.15 / Net I/σ(I): 7.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2649 / Rsym value: 0.664 / % possible all: 95.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1593)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FFS

3ffs


Resolution: 2.415→39.587 Å / SU ML: 0.3 / Isotropic thermal model: MIXED / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2554 5.11 %RANDOM
Rwork0.202 ---
all0.205 49972 --
obs0.205 49972 88.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.2 Å2
Refinement stepCycle: LAST / Resolution: 2.415→39.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10209 0 219 133 10561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110608
X-RAY DIFFRACTIONf_angle_d1.44514302
X-RAY DIFFRACTIONf_dihedral_angle_d11.5143969
X-RAY DIFFRACTIONf_chiral_restr0.0581686
X-RAY DIFFRACTIONf_plane_restr0.0061783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.415-2.46160.3820.21721489157151
2.4616-2.51180.29781110.24091842195362
2.5118-2.56640.30541060.23942019212569
2.5664-2.62610.36061160.2462228234475
2.6261-2.69170.28581220.24112382250481
2.6917-2.76450.3541060.25222580268687
2.7645-2.84580.26951440.23442723286792
2.8458-2.93770.26961540.24432868302296
2.9377-3.04260.28841430.23812941308499
3.0426-3.16440.30781260.22862983310999
3.1644-3.30830.30261740.23482932310699
3.3083-3.48270.29031740.20952915308999
3.4827-3.70070.25941620.19482932309499
3.7007-3.98620.23551680.18512917308598
3.9862-4.38690.22621670.16932937310498
4.3869-5.02060.19781590.15752921308098
5.0206-6.32130.26771770.19622903308098
6.3213-39.59210.20651630.18252906306995
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)
11.36470.2348-0.17551.3897-0.39382.2080.08580.1619-0.3285-0.5206-0.19680.12790.81780.1440.03270.51720.1019-0.06350.2797-0.01990.335914.6087-18.9690.5631
21.71820.5248-0.59121.0785-0.14590.7309-0.05320.2348-0.5155-0.41780.1376-0.67030.45570.52560.14760.55070.6520.39980.7915-0.17480.567334.365-18.5953-9.2255
31.313-0.0779-0.16010.52440.97731.85920.18820.41770.1121-0.95730.0124-0.60150.26530.684-0.13940.76160.1520.24150.6767-0.04070.431327.8336-12.7977-21.4213
41.35740.2404-0.08022.38540.12662.31420.08930.2197-0.0049-0.4327-0.0137-0.0750.34430.1911-0.06510.38690.12150.04180.2919-0.01630.272516.3647-9.3909-7.4956
51.97-0.01950.24782.06850.38341.49760.07740.36920.03690.06040.3641-0.74510.43120.9143-0.27770.54010.28470.08220.7279-0.14750.580935.3577-12.075-0.1896
62.110.27851.53543.5898-0.07944.61070.13680.0099-0.4851-0.01480.1189-0.80820.27540.6572-0.22860.32730.09540.02540.34030.02150.397318.5637-16.729712.1249
71.59090.43841.09613.39072.4934.07550.12280.08520.13410.30250.05360.21650.35680.5704-0.12940.1916-0.0548-0.04770.36020.04520.29355.1746-6.263825.4912
81.74910.06680.34341.602-1.4181.33410.2281-0.109-0.43020.5591-0.2551-0.43351.00510.14730.00080.92280.0569-0.22120.31950.15570.541314.0537-33.385334.2246
91.5844-0.404-0.51592.8503-0.32391.87090.0864-0.0602-0.34360.2113-0.0740.12620.4736-0.0774-0.00470.4545-0.028-0.10420.22760.02080.32527.9486-21.958125.435
103.0388-0.21331.11911.7633-1.5978.09170.08550.0121-0.30260.2573-0.4602-1.0899-0.31810.88530.39030.54540.0965-0.23950.54290.21110.805331.2418-22.437729.2924
113.6553-1.1406-0.65732.6249-0.27210.22830.1348-0.9084-0.3251.2241-0.1863-0.4190.31360.034-0.02990.7351-0.1312-0.20670.44530.04740.292814.1164-12.140643.401
122.30040.8359-0.23793.3054-0.21193.75040.0761-0.3189-0.0370.57090.0181-0.26970.06090.6135-0.11920.43390.0555-0.10150.2997-0.00770.283912.8824-3.364834.3032
132.3110.9925-0.33362.6571-2.26222.65030.16590.1238-0.15670.0454-0.1713-0.2194-0.1913-0.0139-0.07710.15690.0078-0.00120.2906-0.02530.31145.949112.995521.644
141.56730.03840.43481.32420.39841.56010.2563-0.67040.43150.99930.0877-0.0524-0.72720.4359-0.08290.8421-0.192-0.0570.5331-0.20430.334514.088823.492847.2009
152.46330.41780.09675.15530.34550.0427-0.099-0.93510.39231.0520.30060.3853-0.48670.2984-0.30021.0952-0.1083-0.03380.579-0.14960.29858.547817.687257.3128
160.9608-0.7-0.60572.13430.08182.14310.0791-0.35680.11240.7494-0.00910.0978-0.02240.0019-0.06270.4393-0.11970.03370.3743-0.0710.2564.070711.636241.2097
175.18880.885-0.79571.5597-0.70720.4975-0.4024-0.2469-0.16360.22270.8659-0.7740.16951.142-0.42030.6768-0.111-0.17610.949-0.33430.525531.062614.629542.2317
182.49520.54670.19042.1990.57341.39060.3117-0.49080.05221.0443-0.1335-0.1979-0.30980.7854-0.0520.5519-0.1625-0.05380.5997-0.12860.315521.441314.43739.2041
192.8118-0.909-1.00213.10180.05692.4578-0.1088-0.52360.27580.13190.1255-0.5564-0.3070.63720.01810.346-0.1287-0.05230.37160.05010.319216.280819.465121.3416
201.9304-0.4505-0.54463.44181.75342.85320.1957-0.2287-0.0173-0.2537-0.04410.0923-0.11950.49210.06880.16010.0724-0.0490.22280.04950.311810.06138.7323.8461
211.73440.1305-0.01281.5922-0.45720.95260.11890.23040.6575-0.6877-0.1384-0.8212-0.8430.30580.09830.7305-0.21960.23730.35940.14250.686326.59932.8777-3.1045
222.17191.1211-0.8641.1836-0.97720.8496-0.0347-0.02450.3886-0.2089-0.2441-0.427-0.640.27090.26030.7939-0.15960.0110.35180.1090.666718.887340.96814.3149
231.5722-0.75250.27473.0157-0.60532.45460.05730.02720.3417-0.053-0.16210.1944-0.5575-0.04470.11420.3941-0.04180.06060.21850.0080.384510.765630.05176.7746
241.78480.05760.51362.0679-0.31332.2890.1065-0.13540.208-0.0472-0.3015-0.8662-0.25520.60640.10120.3139-0.10960.07880.44810.11640.576329.543221.68135.305
252.0745-0.7845-0.35262.417-0.40873.36950.04990.14680.1086-0.2089-0.0882-0.57890.06780.880.04710.2972-0.0020.03930.3603-0.03440.421821.88145.957-0.7269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 274 )
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 358 )
6X-RAY DIFFRACTION6chain 'A' and (resid 359 through 399 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 25 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 182 )
9X-RAY DIFFRACTION9chain 'B' and (resid 183 through 274 )
10X-RAY DIFFRACTION10chain 'B' and (resid 275 through 340 )
11X-RAY DIFFRACTION11chain 'B' and (resid 341 through 358 )
12X-RAY DIFFRACTION12chain 'B' and (resid 359 through 399 )
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 25 )
14X-RAY DIFFRACTION14chain 'C' and (resid 26 through 89 )
15X-RAY DIFFRACTION15chain 'C' and (resid 90 through 154 )
16X-RAY DIFFRACTION16chain 'C' and (resid 155 through 275 )
17X-RAY DIFFRACTION17chain 'C' and (resid 276 through 300 )
18X-RAY DIFFRACTION18chain 'C' and (resid 301 through 358 )
19X-RAY DIFFRACTION19chain 'C' and (resid 359 through 399 )
20X-RAY DIFFRACTION20chain 'D' and (resid -1 through 25 )
21X-RAY DIFFRACTION21chain 'D' and (resid 26 through 145 )
22X-RAY DIFFRACTION22chain 'D' and (resid 146 through 169 )
23X-RAY DIFFRACTION23chain 'D' and (resid 170 through 245 )
24X-RAY DIFFRACTION24chain 'D' and (resid 246 through 358 )
25X-RAY DIFFRACTION25chain 'D' and (resid 359 through 399 )

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