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

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Basic information

Entry
Database: PDB / ID: 5vsv
TitleCrystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P225
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-8KY / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.205 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 P225
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
DepositionMay 12, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2017ID: 5UZO
Revision 1.0May 24, 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
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)156,76912
Polymers153,7654
Non-polymers3,0048
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21470 Å2
ΔGint-136 kcal/mol
Surface area46520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.861, 77.637, 78.972
Angle α, β, γ (deg.)110.83, 104.05, 105.44
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 38441.266 Da / Num. of mol.: 4
Mutation: CBS domain (residues 89 - 215) is replaced with SGG residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: guaB_2, guaB, ERS852446_02285, JFP838_13815 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: A0A127ELD1, IMP dehydrogenase
#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-8KY / {2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenoxy}acetic acid


Mass: 402.871 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H23ClN2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 17.1% PEG600, 50mM Bicine pH 8.4, 4.3% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.79719 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 27, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79719 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 59509 / % possible obs: 96.3 % / Redundancy: 2 % / Biso Wilson estimate: 30.11 Å2 / Rsym value: 0.148 / Net I/σ(I): 6.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2929 / CC1/2: 0.561 / Rsym value: 0.689 / % possible all: 94.1

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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
Starting model: PDB ID 4Q32

4q32


Resolution: 2.205→37.133 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.57
RfactorNum. reflection% reflection
Rfree0.2411 3003 5.07 %
Rwork0.1977 --
obs0.2 59220 94.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.205→37.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10085 0 204 212 10501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710558
X-RAY DIFFRACTIONf_angle_d0.95614284
X-RAY DIFFRACTIONf_dihedral_angle_d17.4266388
X-RAY DIFFRACTIONf_chiral_restr0.0541646
X-RAY DIFFRACTIONf_plane_restr0.0051830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2053-2.24150.3322900.28781735X-RAY DIFFRACTION60
2.2415-2.28010.34971190.27232659X-RAY DIFFRACTION93
2.2801-2.32160.32021430.26792706X-RAY DIFFRACTION94
2.3216-2.36620.31381280.26242644X-RAY DIFFRACTION95
2.3662-2.41450.29551310.25872770X-RAY DIFFRACTION95
2.4145-2.4670.29891450.24782667X-RAY DIFFRACTION95
2.467-2.52440.31221460.24162749X-RAY DIFFRACTION95
2.5244-2.58750.30721470.23612689X-RAY DIFFRACTION95
2.5875-2.65740.29511340.22782722X-RAY DIFFRACTION96
2.6574-2.73560.28851390.23562757X-RAY DIFFRACTION96
2.7356-2.82390.26221310.23432711X-RAY DIFFRACTION96
2.8239-2.92470.30491650.23492718X-RAY DIFFRACTION96
2.9247-3.04180.33281380.24192758X-RAY DIFFRACTION96
3.0418-3.18020.30241380.22712747X-RAY DIFFRACTION96
3.1802-3.34770.30241610.21852697X-RAY DIFFRACTION97
3.3477-3.55730.24191580.20172750X-RAY DIFFRACTION97
3.5573-3.83170.2261970.17712821X-RAY DIFFRACTION97
3.8317-4.21680.21851790.15462741X-RAY DIFFRACTION98
4.2168-4.82590.17061830.1442745X-RAY DIFFRACTION97
4.8259-6.07580.22311300.15362786X-RAY DIFFRACTION98
6.0758-37.1380.14212010.13972645X-RAY DIFFRACTION95
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)
13.88532.9551.22414.95851.36532.196-0.17350.46330.048-0.4466-0.2624-0.18-0.10990.49120.15810.0661-0.063-0.00740.35220.19060.39249.427412.0608-9.1865
22.3864-0.41370.82741.7812-1.16852.0963-0.410.11040.4231-0.0386-0.1027-0.1826-0.8431-0.11980.45760.56290.0663-0.19710.26970.00740.404-9.208632.9093-16.8502
31.35190.02410.07161.62560.27310.5073-0.37470.24890.3862-0.1378-0.0921-0.195-0.3912-0.03030.25260.48530.0404-0.13990.2650.04970.3385-13.555428.1753-27.8774
41.66390.02721.12791.365-0.7571.889-0.17380.26210.1044-0.086-0.1559-0.2439-0.39450.31320.33970.26190.0002-0.01440.22610.05120.2435-2.412918.2442-22.4868
52.32880.21841.2822.01970.04472.0819-0.3256-0.73490.40290.3493-0.17050.1605-0.4925-0.53510.46530.43360.1539-0.04290.3419-0.03930.3063-13.528223.6746-4.9817
62.6220.4709-0.90462.9913-0.44835.2706-0.0707-0.140.28860.2253-0.1812-0.0127-0.17370.08140.19630.27750.059-0.15720.31470.07240.41065.98217.5830.0177
71.0538-0.27530.83862.26040.28411.2488-0.0797-0.06210.15850.1277-0.1631-0.199-0.34960.24840.25020.4074-0.0214-0.08060.33870.07990.279620.4327.493618.3937
82.49610.1541-0.21381.6413-0.12971.71910.1957-0.58610.98970.4683-0.0309-0.12-0.5679-0.66380.47750.7647-0.1538-0.37420.4295-0.07810.528620.784227.657425.061
92.27210.09340.97780.90470.27011.3193-0.4166-0.2661.25630.3419-0.34-0.031-0.541-0.00210.30840.6414-0.1696-0.29340.42220.11890.701524.95229.265516.1346
101.74580.01920.19151.9085-0.14111.293-0.2260.1460.34720.0653-0.1132-0.3432-0.24890.31320.29010.3579-0.054-0.13150.3320.12950.37722.339316.22868.3985
111.9417-1.0850.27263.373-0.72793.904-0.2774-0.19250.09820.62350.08390.0434-0.46-0.36350.29990.54870.0226-0.16810.3149-0.0720.37112.593520.157921.4858
120.9647-0.29990.89311.42580.18331.6181-0.0327-0.08190.04680.1704-0.0592-0.0723-0.02090.11930.08920.3394-0.0155-0.03730.23910.09540.285217.4033-1.863516.3957
135.68371.76011.18661.32930.40972.16540.0507-0.80481.4472-0.0617-0.11920.2765-0.4032-0.35650.07630.63780.0436-0.0410.3907-0.08460.3373-0.528-3.124220.7774
142.82560.40460.96113.0051-1.02911.04460.0472-0.1309-0.1763-0.35840.13790.40260.1082-0.1063-0.19780.26670.0273-0.00050.21580.0060.184-18.9197-10.7758-19.6068
151.8043-0.04180.81432.01060.72472.10040.22890.0832-0.5181-0.1410.07440.32620.583-0.1031-0.30750.4694-0.0463-0.15230.23280.07650.4415-21.0545-27.2454-18.0616
161.0772-0.65690.77431.1796-1.03412.2014-0.0787-0.1067-0.17830.30980.20860.1759-0.0782-0.2589-0.13170.2928-0.0127-0.00230.19410.05790.2842-18.5691-10.326-10.8965
172.277-0.08242.06913.61180.93942.7005-0.01940.05110.0701-0.125-0.02240.0309-0.216-0.0120.00560.1557-0.02570.05850.16770.06980.2175-10.6583.5725-14.922
182.02541.5821.1552.09710.83671.95090.174-0.0461-0.0945-0.155-0.19310.18060.44830.1532-0.01680.54540.1239-0.09060.2021-0.02880.34140.2496-23.4422-1.6042
192.0982-0.15920.99272.6687-0.13881.13490.2636-0.3813-0.32060.0556-0.03570.19990.3338-0.1396-0.19370.5062-0.0677-0.11240.25550.08470.31693.1288-29.251725.8814
202.4260.60730.06481.0241-0.05191.18430.1453-0.0327-0.16980.15380.0547-0.03670.70550.5713-0.10280.60960.0243-0.16980.30850.01580.322314.3136-27.38828.2616
211.0828-0.49541.47791.333-0.80112.56740.22950.0753-0.1704-0.0855-0.0773-0.03480.40530.2146-0.11980.41520.0775-0.05830.23980.01720.259312.9674-22.06713.8989
226.74542.1381.46022.247-0.28183.13390.1734-0.42410.55810.4614-0.05870.47770.0555-0.4016-0.08020.44650.05310.06790.33060.02140.2965-5.6058-12.856625.7535
230.1212-0.25920.16590.9861.30294.88120.252-0.0097-0.13390.0386-0.07020.14480.5778-0.1851-0.09310.4916-0.0685-0.15280.22730.08570.4314-8.8123-27.5237.4913
243.11040.76250.38521.0368-1.11392.79220.33390.030.02160.028-0.0493-0.0226-0.0491-0.0468-0.28250.40920.0172-0.07110.1969-0.00930.1746-6.0237-16.8878-0.2342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 252 )
4X-RAY DIFFRACTION4chain 'A' and (resid 253 through 358 )
5X-RAY DIFFRACTION5chain 'A' and (resid 359 through 440 )
6X-RAY DIFFRACTION6chain 'A' and (resid 441 through 481 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 63 )
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 227 )
9X-RAY DIFFRACTION9chain 'B' and (resid 228 through 252 )
10X-RAY DIFFRACTION10chain 'B' and (resid 253 through 358 )
11X-RAY DIFFRACTION11chain 'B' and (resid 359 through 422 )
12X-RAY DIFFRACTION12chain 'B' and (resid 423 through 465 )
13X-RAY DIFFRACTION13chain 'B' and (resid 466 through 481 )
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 75 )
15X-RAY DIFFRACTION15chain 'C' and (resid 76 through 304 )
16X-RAY DIFFRACTION16chain 'C' and (resid 305 through 440 )
17X-RAY DIFFRACTION17chain 'C' and (resid 441 through 481 )
18X-RAY DIFFRACTION18chain 'D' and (resid 5 through 31 )
19X-RAY DIFFRACTION19chain 'D' and (resid 32 through 227 )
20X-RAY DIFFRACTION20chain 'D' and (resid 228 through 252 )
21X-RAY DIFFRACTION21chain 'D' and (resid 253 through 358 )
22X-RAY DIFFRACTION22chain 'D' and (resid 359 through 422 )
23X-RAY DIFFRACTION23chain 'D' and (resid 423 through 440 )
24X-RAY DIFFRACTION24chain 'D' and (resid 441 through 481 )

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