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- PDB-5uzs: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 5uzs
TitleCrystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P200
ComponentsInosine-5'-monophosphate dehydrogenase
Keywordsoxidoreductase/oxidoreductase inhibitor / TIM barrel / IMPDH / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / OXIDOREDUCTASE / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-8L4 / INOSINIC ACID / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.367 Å
AuthorsMaltseva, N. / Kim, Y. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D.R. / Hedstrom, L. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P200
Authors: Maltseva, N. / Kim, Y. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D.R. / Hedstrom, L. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)158,51829
Polymers153,9294
Non-polymers4,58925
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26970 Å2
ΔGint-109 kcal/mol
Surface area47170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.124, 144.396, 87.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-505-

MG

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 38482.297 Da / Num. of mol.: 4
Mutation: CBS domain (residues 89-215) is replaced by residues SGG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A) (bacteria)
Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A
Gene: guaB, CPF_2558 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: A0A0H2YRZ7, IMP dehydrogenase

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Non-polymers , 9 types, 172 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-8L4 / 3-(2-{[(4-chlorophenyl)carbamoyl]amino}propan-2-yl)-N-hydroxybenzene-1-carboximidamide


Mass: 346.811 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H19ClN4O2
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 0.05M acetate pH 5.2, 45% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 14, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 59812 / % possible obs: 99.9 % / Redundancy: 17.03 % / Biso Wilson estimate: 32.97 Å2 / Rsym value: 0.125 / Net I/σ(I): 8
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 7.9 / Num. unique obs: 2954 / CC1/2: 0.861 / Rsym value: 0.699 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.367→31.087 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.78
RfactorNum. reflection% reflection
Rfree0.2377 2838 4.96 %
Rwork0.17 --
obs0.1734 57229 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.7 Å2
Refinement stepCycle: LAST / Resolution: 2.367→31.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10214 0 304 147 10665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810836
X-RAY DIFFRACTIONf_angle_d1.0214613
X-RAY DIFFRACTIONf_dihedral_angle_d25.54079
X-RAY DIFFRACTIONf_chiral_restr0.0581673
X-RAY DIFFRACTIONf_plane_restr0.0051867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3668-2.40760.2937950.21852005X-RAY DIFFRACTION74
2.4076-2.45130.30611500.20922663X-RAY DIFFRACTION99
2.4513-2.49850.29021480.19722742X-RAY DIFFRACTION100
2.4985-2.54940.26841560.18962675X-RAY DIFFRACTION100
2.5494-2.60480.25181340.18352740X-RAY DIFFRACTION100
2.6048-2.66540.26851460.18762730X-RAY DIFFRACTION100
2.6654-2.7320.2641420.19162732X-RAY DIFFRACTION100
2.732-2.80580.25771640.1932704X-RAY DIFFRACTION100
2.8058-2.88840.29691420.19532740X-RAY DIFFRACTION100
2.8884-2.98150.29911250.20982735X-RAY DIFFRACTION100
2.9815-3.0880.30691440.21472750X-RAY DIFFRACTION100
3.088-3.21150.29791270.21022761X-RAY DIFFRACTION100
3.2115-3.35750.29871490.20032758X-RAY DIFFRACTION100
3.3575-3.53430.23751550.18312734X-RAY DIFFRACTION100
3.5343-3.75540.20841280.16142769X-RAY DIFFRACTION100
3.7554-4.04470.21051410.14312795X-RAY DIFFRACTION100
4.0447-4.45070.17191210.13632810X-RAY DIFFRACTION100
4.4507-5.09230.18331450.12462801X-RAY DIFFRACTION100
5.0923-6.40660.22051620.1562816X-RAY DIFFRACTION100
6.4066-31.08980.1881640.14462931X-RAY DIFFRACTION99
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)
10.47630.19010.42361.02510.46310.70860.3079-0.54260.11340.4091-0.27490.10580.1135-0.2302-0.05290.5213-0.21750.08990.5611-0.07870.3043-9.80220.149744.0486
21.3864-0.74750.76021.7903-0.44910.4166-0.1194-0.1640.4740.177-0.21390.6860.134-0.82540.25820.7008-0.32210.1690.7493-0.27540.3924-6.739738.474554.1435
32.3211-2.1502-3.96682.14453.32659.06860.2152-0.2250.06940.4914-0.4209-0.3525-0.2047-0.21060.20620.4742-0.2208-0.00830.463-0.06920.29970.983235.370948.8055
40.78870.3992-0.05721.02580.2041.85630.2063-0.27540.2130.2749-0.19720.06310.0436-0.131-0.00710.3719-0.16650.04390.3968-0.10.2757-6.693726.049340.2911
51.3548-0.1785-0.57513.3279-1.07463.31020.1377-0.39050.30260.3632-0.10360.27-0.0097-0.6513-0.03740.4134-0.22210.07220.5887-0.17870.3444-19.479725.401841.8056
63.30130.53130.01721.5158-0.75072.39140.168-0.39980.35610.2488-0.10260.13030.0631-0.2148-0.0370.4652-0.17410.07840.3334-0.08810.2402-20.61669.233235.8672
76.91262.93094.67942.313.23874.18670.41-0.482-0.14970.3131-0.1588-0.22840.3832-0.1798-0.24220.3414-0.05250.03020.21330.05380.1757-16.3327-3.55521.921
81.6522-0.1082-0.96171.2612-0.4433.69330.0694-0.2267-0.05650.4757-0.10860.3088-0.092-0.20090.04620.3265-0.12080.09570.3231-0.00470.3244-41.7949-10.838635.3086
92.7520.34811.35311.20310.95061.2528-0.049-0.5165-0.00710.3351-0.22220.2625-0.06840.19550.24830.6314-0.21260.1230.5150.03840.3438-35.2347-11.225646.706
101.29180.1131-0.33640.97860.35740.78650.1598-0.223-0.0070.2798-0.178-0.1079-0.06440.1630.01310.3426-0.12210.03390.3350.0280.244-25.9292-7.949835.0627
117.96071.89433.22546.3857-1.0556.4354-0.60280.42190.9535-0.0590.37490.5868-1.1949-0.29520.23320.48860.02770.08940.33290.01770.5891-47.86129.2329.7411
121.52210.16970.19581.96141.11234.09950.1435-0.34380.12750.1269-0.14040.146-0.6384-0.04640.02660.3162-0.05750.10650.2863-0.02620.2796-38.12050.96827.7125
134.4453-0.21560.05766.8327-1.43122.50760.08570.06740.3769-0.16830.00960.1866-0.1782-0.0891-0.07610.2279-0.03720.06040.2252-0.03380.0908-28.083-0.56113.2025
140.68450.3046-0.09631.03790.00630.70580.0352-0.00820.2631-0.0391-0.0170.0663-0.15960.0693-0.01670.2196-0.01450.01790.2417-00.36290.022136.24754.2755
151.5179-1.48820.13764.13142.05112.010.0560.19540.319-0.2230.07270.1681-0.20970.1588-0.13570.2144-0.04640.05020.28890.10370.33042.675336.5952-9.9932
163.26921.2395-0.84682.3485-1.18242.9080.04530.14080.1079-0.0656-0.0189-0.10850.1280.1839-0.01940.1640.00850.00450.1416-0.00570.27663.38925.0963-2.0583
171.9804-1.64180.75092.1671-0.04591.03450.0351-0.09640.3249-0.0006-0.0010.1205-0.073-0.1851-0.03860.2355-0.0380.0530.2545-0.01150.4023-9.839436.67369.0156
181.4498-0.33980.31551.39820.24291.2986-0.0148-0.06240.3409-0.0287-0.11870.2663-0.1572-0.27970.15590.1788-0.05730.04520.22590.02510.379-10.626636.67488.1915
195.3925-0.2433-1.54994.71750.77942.33160.0812-0.2787-0.08020.0645-0.15780.41930.0346-0.28720.08410.291-0.0793-0.01460.2928-0.05480.1006-6.589327.564823.49
201.16810.6516-0.04320.81890.07710.7748-0.16550.17960.1695-0.18420.13420.0631-0.10160.08290.03930.231-0.02710.01670.24040.02190.2225-21.77144.7856-7.7582
217.61392.468-1.88487.09-3.40649.0339-0.29290.51810.3856-0.76090.25240.727-0.1801-0.69290.03490.3156-0.0327-0.0910.2982-0.04410.2732-38.6392-2.7929-17.4971
223.9198-0.75182.11133.1167-4.96728.2664-0.30440.10860.0508-0.28330.10370.09310.088-0.22230.24020.2307-0.0149-0.03780.173-0.04670.2837-33.9006-9.5606-12.192
231.35870.43690.3971.6094-0.22940.9868-0.11960.05120.0835-0.08350.10180.0421-0.09890.03970.00850.1501-0.0297-0.00880.17630.01760.205-25.5815-0.4918-4.1985
245.63551.7083-1.98851.845-1.78073.1323-0.18110.26580.2122-0.05960.2340.2728-0.0333-0.3722-0.08010.2475-0.0187-0.03820.1278-0.03160.284-30.941711.1696-3.7353
250.4182-0.52770.37155.11920.65092.39570.0308-0.0810.11610.0442-0.00730.3596-0.1017-0.2103-0.02190.1779-0.06020.03480.29520.00730.3099-14.303217.60430.7181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 227 )
3X-RAY DIFFRACTION3chain 'A' and (resid 228 through 252 )
4X-RAY DIFFRACTION4chain 'A' and (resid 253 through 393 )
5X-RAY DIFFRACTION5chain 'A' and (resid 394 through 440 )
6X-RAY DIFFRACTION6chain 'A' and (resid 441 through 480 )
7X-RAY DIFFRACTION7chain 'B' and (resid -2 through 24 )
8X-RAY DIFFRACTION8chain 'B' and (resid 25 through 227 )
9X-RAY DIFFRACTION9chain 'B' and (resid 228 through 252 )
10X-RAY DIFFRACTION10chain 'B' and (resid 253 through 363 )
11X-RAY DIFFRACTION11chain 'B' and (resid 364 through 384 )
12X-RAY DIFFRACTION12chain 'B' and (resid 385 through 441 )
13X-RAY DIFFRACTION13chain 'B' and (resid 442 through 480 )
14X-RAY DIFFRACTION14chain 'C' and (resid -2 through 227 )
15X-RAY DIFFRACTION15chain 'C' and (resid 228 through 252 )
16X-RAY DIFFRACTION16chain 'C' and (resid 253 through 329 )
17X-RAY DIFFRACTION17chain 'C' and (resid 330 through 384 )
18X-RAY DIFFRACTION18chain 'C' and (resid 385 through 441 )
19X-RAY DIFFRACTION19chain 'C' and (resid 442 through 481 )
20X-RAY DIFFRACTION20chain 'D' and (resid -2 through 75 )
21X-RAY DIFFRACTION21chain 'D' and (resid 76 through 227 )
22X-RAY DIFFRACTION22chain 'D' and (resid 228 through 252 )
23X-RAY DIFFRACTION23chain 'D' and (resid 253 through 384 )
24X-RAY DIFFRACTION24chain 'D' and (resid 385 through 441 )
25X-RAY DIFFRACTION25chain 'D' and (resid 442 through 481 )

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