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- PDB-4my8: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase w... -

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Basic information

Entry
Database: PDB / ID: 4my8
TitleCrystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor Q21
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 / TIM barrel / alpha-beta structure / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / 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 / 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
ACETIC ACID / FORMIC ACID / INOSINIC ACID / Chem-Q21 / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2924 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Gorla, S.K. / Kavitha, M. / Cuny, G. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2013
Title: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor Q21
Authors: Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Gorla, S.K. / Kavitha, M. / Cuny, G. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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)166,73028
Polymers162,8384
Non-polymers3,89124
Water5,386299
1
A: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,85430
Polymers162,8384
Non-polymers4,01526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area21340 Å2
ΔGint-83 kcal/mol
Surface area46860 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,60526
Polymers162,8384
Non-polymers3,76722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area20470 Å2
ΔGint-87 kcal/mol
Surface area47300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.433, 56.226, 111.395
Angle α, β, γ (deg.)90.00, 89.83, 90.00
Int Tables number3
Space group name H-MP121

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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: 40709.574 Da / Num. of mol.: 4 / Fragment: IMPDH-delta-L-CBS / Mutation: replaced residues 92-220 with GG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: guaB, BA_0008, BAS0011, GBAA_0008 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q81W29, UniProt: A0A6L8P2U9*PLUS, IMP dehydrogenase

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Non-polymers , 6 types, 323 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-Q21 / (2S)-2-(naphthalen-1-yloxy)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]propanamide


Mass: 409.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H19N3O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M di-sodium hydrogen phosphate pH 6.2, 10% w/v PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.292→50 Å / Num. all: 59534 / Num. obs: 59534 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 39.34 Å2 / Rsym value: 0.118 / Net I/σ(I): 7.5
Reflection shellResolution: 2.292→2.34 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2462 / Rsym value: 0.45 / % possible all: 79.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID ENTRY 3TSD

3tsd


Resolution: 2.2924→49.879 Å / SU ML: 0.28 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2997 5.06 %random
Rwork0.173 ---
all0.176 59277 --
obs0.176 59277 94.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2924→49.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9723 0 272 299 10294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810219
X-RAY DIFFRACTIONf_angle_d1.15513808
X-RAY DIFFRACTIONf_dihedral_angle_d15.0473712
X-RAY DIFFRACTIONf_chiral_restr0.071601
X-RAY DIFFRACTIONf_plane_restr0.0041764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2924-2.330.33031040.24741991209570
2.33-2.37020.34591250.242357248285
2.3702-2.41330.29161280.22052484261289
2.4133-2.45970.30241180.22962598271692
2.4597-2.50990.3011490.22422580272993
2.5099-2.56450.3331280.21432644277294
2.5645-2.62410.28351460.20242654280094
2.6241-2.68980.2521310.20032694282595
2.6898-2.76250.27591530.19812676282996
2.7625-2.84380.26521620.1992733289597
2.8438-2.93550.24151570.20062771292898
2.9355-3.04040.28141480.20042762291099
3.0404-3.16220.22181320.19952799293199
3.1622-3.3060.23041520.1892809296199
3.306-3.48030.22861680.17327992967100
3.4803-3.69830.19451380.16362804294299
3.6983-3.98370.21831580.14972830298899
3.9837-4.38440.1771560.13332792294899
4.3844-5.01830.17721490.12482832298199
5.0183-6.32050.20411470.16582829297698
6.3205-49.89090.19931480.16782842299095
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)
18.8243-1.8947-2.19830.51540.19530.9846-0.10550.00930.3413-0.0590.0787-0.02980.0302-0.03950.01710.31080.0008-0.01580.20370.01750.36766.029611.414110.9542
25.59231.8458-0.37854.343-0.58113.5657-0.026-0.1287-0.26090.2809-0.0046-0.1915-0.12280.11720.03240.21520.0767-0.02730.27720.04540.183420.51720.221628.4793
33.8875-0.4497-1.1511.893-0.23814.122-0.3815-0.5452-0.730.23020.02730.00440.57320.1510.29650.36150.06410.02280.40.1210.257914.9247-8.98939.5461
42.2431.0756-1.28097.6121-0.67959.0763-0.2856-1.448-0.0230.54980.32930.51160.058-0.5653-0.06880.34140.01780.03190.60670.00350.28778.7202-1.326344.3029
54.2285-1.46132.01062.7595-1.66935.5769-0.1268-0.6031-0.15660.35350.17750.2587-0.265-0.4008-0.0150.25810.0320.00060.3395-0.03020.19954.87468.805137.1329
65.07220.0386-0.70480.1837-0.51641.2794-0.06240.0925-0.10770.0172-0.02-0.01530.05190.05440.11530.26590.02830.00680.2049-0.00440.22438.05765.346321.695
74.8581-0.09840.66014.6277-1.81611.56980.0603-0.0671-0.7744-0.20980.26360.37140.3152-0.0545-0.21830.3981-0.028-0.02070.3137-0.02110.60457.0883-17.683625.7298
84.10090.7393-1.19752.5723-0.99310.8922-0.03920.223-0.48940.0443-0.0284-0.11370.22580.01980.07120.4171-0.0118-0.03030.2787-0.07490.199513.5085-8.499821.0967
92.3015-1.13732.5592.3708-2.2618.2451-0.1074-0.14640.2439-0.2786-0.222-0.06060.2146-0.3650.18270.2983-0.00810.07750.2918-0.04110.202617.37898.736210.4306
106.85822.172-3.03961.2425-1.14322.4778-0.0545-0.2513-0.04610.0558-0.037-0.0735-0.2550.01570.10860.36550.0463-0.00740.2042-0.040.324348.976540.031845.1277
114.150.1506-0.83063.5580.39934.2599-0.03660.447-0.2795-0.36460.1197-0.1878-0.0020.1486-0.05560.221-0.0472-0.01310.3-0.04880.214937.546624.686520.254
122.67021.54033.05932.92053.01125.8512-0.06830.56820.0332-0.26050.2857-0.1178-0.09290.4794-0.19150.265-0.02880.0220.42070.03340.232747.86437.550518.9795
134.81260.0091-0.37630.24360.67361.5815-0.072-0.0835-0.23470.02240.09120.01190.0182-0.02470.00740.2732-0.00310.00970.210.01820.209446.844834.116734.9071
142.544-0.0976-0.12191.0335-0.06593.2817-0.1442-0.1694-0.8552-0.16250.3087-0.67920.9170.0093-0.17610.4611-0.0211-0.05010.30960.06390.611142.63181432.6859
153.71944.8877-0.79016.3825-0.84220.70870.41290.003-1.2835-0.3393-0.361-1.1691-0.21120.39820.01210.4559-0.027-0.06430.47740.01280.737252.388315.005629.3209
163.75422.65690.05044.46392.42955.65670.028-0.0927-0.07670.11490.0344-0.01220.2194-0.0245-0.04660.20470.03380.01020.27260.06010.204934.076832.011443.546
172.263-0.86343.23971.8763-0.33056.66880.11430.02210.182-0.143-0.2833-0.09350.42180.14260.1850.1762-0.06220.08420.2538-0.02030.317245.373740.039562.5949
185.38111.95450.93973.76940.77812.98050.0179-0.1514-0.14510.03380.0420.06440.1473-0.2327-0.06040.2953-0.0010.07280.24370.03830.191826.409325.26276.4591
196.17461.4110.93815.0110.323.07410.0392-0.2567-0.3396-0.03460.21050.63540.8045-1.0365-0.18290.2955-0.1494-0.00230.50070.03640.335814.05421.576272.6658
202.92933.5134-1.79746.6211-3.10363.9982-0.14390.64770.3263-0.73360.39810.49720.1099-1.2801-0.16860.41620.0342-0.01710.55440.06610.307814.66630.121664.8688
212.96580.8031-1.50212.14440.39662.807-0.06960.26820.2494-0.1830.16370.20790.1-0.3716-0.10380.23890.02-0.03110.34080.07820.227622.125737.280363.0675
221.9430.62820.77660.2377-0.51076.86070.0166-0.0773-0.0015-0.0180.0405-0.0652-0.12220.1178-0.08350.2063-0.01170.01610.23350.01260.286436.551835.073565.3813
232.4861-0.62740.90181.6769-0.27832.2460.0757-0.1434-0.867-0.6591-0.1810.02840.96660.08280.04640.67540.04530.1380.2860.03650.50533.084413.881768.6455
242.9381-1.33581.73445.7377-4.47353.56990.27770.3566-0.7313-0.76960.1430.78131.0527-0.1323-0.51160.5566-0.0140.02960.45610.03610.506429.204815.391558.293
255.38355.45311.71485.64341.59483.5860.3126-0.0268-0.30390.6618-0.23020.02940.46730.0802-0.06050.27950.01480.07750.26440.01620.319741.012125.392481.2394
267.61952.5178-1.23724.2363-2.67428.86150.23930.44490.43150.03740.0061-0.1026-0.3786-0.1076-0.20520.25090.0119-0.04570.14180.01210.270345.938337.913874.7416
271.1755-0.1085-0.05880.5299-0.07472.1359-0.02080.13940.0211-0.0551-0.0047-0.0297-0.03460.05030.00470.2751-0.01060.05120.18270.03310.273619.76465.7954-13.2995
285.75671.22140.1234.32320.10524.33190.1432-0.0551-0.69280.2074-0.0011-0.63440.40970.8103-0.12180.26980.07660.01690.4077-0.02590.32141.0606-6.0611-12.6406
298.2985-3.6669-5.61982.92992.59493.9533-0.2445-0.3774-0.09620.41820.119-0.13830.59310.22440.12470.2993-0.05020.00210.3839-0.02450.229239.43386.7604-3.7063
301.7054-0.1821-0.32490.5975-0.04023.3014-0.01830.03340.0017-0.01860.1256-0.01230.0545-0.0088-0.10750.2216-0.00690.0060.2191-0.01810.224224.85216.9919-7.4211
310.9677-0.0377-0.8022.78552.25955.8743-0.00610.0237-0.40850.40910.1645-0.22290.9569-0.097-0.26120.511-0.0070.02630.31780.01080.424425.4819-16.3889-5.5416
325.1434-3.4964-1.11734.59683.32093.54620.0062-0.0513-0.2167-0.189-0.14410.1344-0.0726-0.17480.10940.1747-0.03850.00090.21380.01050.193713.13233.2255-20.4128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 242 )
5X-RAY DIFFRACTION5chain 'A' and (resid 243 through 293 )
6X-RAY DIFFRACTION6chain 'A' and (resid 294 through 363 )
7X-RAY DIFFRACTION7chain 'A' and (resid 364 through 399 )
8X-RAY DIFFRACTION8chain 'A' and (resid 400 through 446 )
9X-RAY DIFFRACTION9chain 'A' and (resid 447 through 470 )
10X-RAY DIFFRACTION10chain 'B' and (resid -1 through 26 )
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 242 )
12X-RAY DIFFRACTION12chain 'B' and (resid 243 through 293 )
13X-RAY DIFFRACTION13chain 'B' and (resid 294 through 355 )
14X-RAY DIFFRACTION14chain 'B' and (resid 356 through 389 )
15X-RAY DIFFRACTION15chain 'B' and (resid 390 through 427 )
16X-RAY DIFFRACTION16chain 'B' and (resid 428 through 469 )
17X-RAY DIFFRACTION17chain 'C' and (resid -1 through 26 )
18X-RAY DIFFRACTION18chain 'C' and (resid 27 through 77 )
19X-RAY DIFFRACTION19chain 'C' and (resid 78 through 230 )
20X-RAY DIFFRACTION20chain 'C' and (resid 231 through 257 )
21X-RAY DIFFRACTION21chain 'C' and (resid 258 through 309 )
22X-RAY DIFFRACTION22chain 'C' and (resid 310 through 355 )
23X-RAY DIFFRACTION23chain 'C' and (resid 356 through 389 )
24X-RAY DIFFRACTION24chain 'C' and (resid 390 through 427 )
25X-RAY DIFFRACTION25chain 'C' and (resid 428 through 446 )
26X-RAY DIFFRACTION26chain 'C' and (resid 447 through 469 )
27X-RAY DIFFRACTION27chain 'D' and (resid -1 through 56 )
28X-RAY DIFFRACTION28chain 'D' and (resid 57 through 242 )
29X-RAY DIFFRACTION29chain 'D' and (resid 243 through 270 )
30X-RAY DIFFRACTION30chain 'D' and (resid 271 through 363 )
31X-RAY DIFFRACTION31chain 'D' and (resid 364 through 427 )
32X-RAY DIFFRACTION32chain 'D' and (resid 428 through 471 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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