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

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Basic information

Entry
Database: PDB / ID: 5uze
TitleCrystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P182
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-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-8L1 / INOSINIC ACID / : / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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)
CitationJournal: To Be Published
Title: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P182
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 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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,Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,31615
Polymers153,7654
Non-polymers3,55111
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21770 Å2
ΔGint-125 kcal/mol
Surface area46470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.777, 77.662, 80.321
Angle α, β, γ (deg.)110.03, 103.99, 105.46
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Inosine-5'-monophosphate dehydrogenase,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 (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): BL(DE3)magic / References: UniProt: A0A0H2YRZ7, IMP dehydrogenase

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Non-polymers , 5 types, 167 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-8L1 / N-{4-chloro-3-[4-(trifluoromethyl)-1,3-thiazol-2-yl]phenyl}-N'-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea


Mass: 496.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H20ClF3N4O2S
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 20% PEG600, 50mM ADA pH 6.8

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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: Feb 27, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 60049 / % possible obs: 97.3 % / Redundancy: 2.1 % / Biso Wilson estimate: 36.18 Å2 / Rsym value: 0.083 / Net I/σ(I): 8.9
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2992 / CC1/2: 0.784 / Rsym value: 0.502 / % possible all: 97

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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: 2.27→31.387 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.03
RfactorNum. reflection% reflection
Rfree0.2553 2855 4.8 %
Rwork0.1939 --
obs0.197 59418 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.27→31.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10075 0 232 156 10463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910451
X-RAY DIFFRACTIONf_angle_d1.22414134
X-RAY DIFFRACTIONf_dihedral_angle_d23.7233866
X-RAY DIFFRACTIONf_chiral_restr0.0641635
X-RAY DIFFRACTIONf_plane_restr0.0061797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2512-2.290.37681060.27742178X-RAY DIFFRACTION72
2.29-2.33170.33621570.27892816X-RAY DIFFRACTION96
2.3317-2.37650.36251390.26582851X-RAY DIFFRACTION96
2.3765-2.4250.34771460.2562888X-RAY DIFFRACTION96
2.425-2.47770.33481340.2462829X-RAY DIFFRACTION96
2.4777-2.53530.32081390.22632870X-RAY DIFFRACTION96
2.5353-2.59870.29161560.23542876X-RAY DIFFRACTION96
2.5987-2.66890.30581240.22692883X-RAY DIFFRACTION96
2.6689-2.74740.33041390.24712861X-RAY DIFFRACTION96
2.7474-2.8360.34251180.23772868X-RAY DIFFRACTION96
2.836-2.93730.3241420.23452872X-RAY DIFFRACTION96
2.9373-3.05480.29721720.23562780X-RAY DIFFRACTION96
3.0548-3.19370.30691430.2252867X-RAY DIFFRACTION96
3.1937-3.36190.28161230.22612937X-RAY DIFFRACTION97
3.3619-3.57230.32811230.19242873X-RAY DIFFRACTION97
3.5723-3.84760.24351670.18572851X-RAY DIFFRACTION97
3.8476-4.2340.18541580.1522872X-RAY DIFFRACTION97
4.234-4.84470.20581750.14122846X-RAY DIFFRACTION97
4.8447-6.09650.18941370.16092937X-RAY DIFFRACTION98
6.0965-31.38980.19731570.14852808X-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)
12.87491.5042-0.87412.0689-0.51021.4155-0.02160.2238-0.1201-0.43980.190.13380.4064-0.3882-0.20070.5175-0.09270.04740.2468-0.04050.2743-9.8883-4.8129-22.8975
22.9198-0.09250.31764.09450.48662.8085-0.23570.2679-0.1649-0.41110.24780.76140.2161-0.4511-0.01590.397-0.1562-0.06560.37240.05310.4988-30.3998-19.6633-16.7836
33.3326-1.87450.61671.7501-1.14841.4279-0.012-0.1336-0.6777-0.61810.1586-0.11820.5554-0.3163-0.16070.52-0.15480.02710.301-0.05450.5021-24.1404-29.5265-17.0584
42.36711.790.90943.01981.442.1485-0.3380.4222-0.5275-0.37730.4076-0.23530.29470.1622-0.08960.3643-0.02960.08640.2305-0.06980.4352-11.2575-23.8439-16.7822
52.29710.4898-0.7011.3343-0.48622.3781-0.19180.1544-0.087-0.16270.26430.31420.1892-0.3234-0.08740.2921-0.0706-0.03940.23220.05940.3756-22.5518-8.3247-9.6317
64.77920.05690.9653.1790.95051.9835-0.2767-0.0020.1516-0.2480.29980.0948-0.038-0.1808-0.00830.3567-0.061-0.01510.16470.11540.217-10.87423.693-14.6562
78.95975.89774.44646.82714.28956.46020.01810.14920.0945-0.0335-0.0098-0.1850.28040.0843-0.07060.16920.02580.00660.22130.01120.20379.763612.1341-8.8327
83.1586-0.39870.74131.3364-0.98081.6367-0.32740.16550.7257-0.02970.25590.4429-0.3849-0.07210.09980.4617-0.0047-0.03480.22340.08340.6966-5.100131.7453-15.7033
91.3344-0.11240.34064.5169-1.2232.115-0.27670.43960.6052-0.28250.32730.5609-0.1212-0.2701-0.06480.4337-0.1117-0.14380.43580.2260.5758-10.369126.8418-29.0594
102.17741.24270.17971.0214-0.39070.7756-0.22340.23760.2753-0.1730.19460.1835-0.1169-0.05180.01860.29230.0016-0.04560.17080.0430.3277-1.153816.9282-16.2063
113.3270.09660.27922.0906-0.08991.69110.0029-0.35930.51650.03240.18760.6467-0.1609-0.5038-0.14860.33080.07370.03670.29480.06730.5469-13.647523.8654-5.4528
123.60460.5747-0.85183.0943-1.02565.77570.0218-0.30790.39860.01220.0030.1387-0.24520.0594-0.05360.2128-0.0156-0.05740.1545-0.06230.3126.412417.5655-0.1902
131.60531.76241.12164.58121.14052.771-0.1601-0.1284-0.3391-0.1419-0.08520.01580.20330.3170.15040.2840.0948-0.00440.17960.04560.48564.148-17.1234-2.1508
141.906-0.37390.07582.0683-0.22061.88640.029-0.9728-0.8420.3553-0.171-0.22350.49720.06870.07570.5895-0.0357-0.06810.63570.40570.8351.6597-29.991824.3513
150.5671-0.95990.75211.6424-1.27642.0880.1523-0.5344-0.46420.21670.0176-0.260.2640.29350.64280.45320.1407-0.2730.69840.71340.993216.4173-27.693925.7522
161.1241-0.41490.75661.9005-0.32551.57630.1654-0.4308-0.7019-0.0837-0.18-0.47130.20840.20740.0040.39290.0627-0.03340.35640.16450.600910.4286-19.507410.7908
171.27770.935-0.46762.0563-0.14323.8560.1529-0.4199-0.40740.3973-0.09240.07850.178-0.0418-0.07730.31820.0114-0.03760.40530.18610.4606-6.7169-17.917520.0576
181.54750.0523-0.11124.6113-0.39232.817-0.0312-0.1616-0.5048-0.0430.0864-0.1480.1874-0.1072-0.07420.338-0.0063-0.02340.22870.0720.3993-6.6822-17.18860.3881
195.1456-2.62394.39924.843-1.97836.42060.27950.1234-0.47-0.2589-0.4968-0.60910.16880.7280.16770.17590.02840.04530.26210.10170.449716.528-2.10176.3923
202.1436-0.353-0.56062.37150.34090.85320.221-1.1018-0.05410.6537-0.3331-0.4046-0.22890.2936-0.00170.6027-0.1708-0.15130.8917-0.08980.312121.149915.554124.2077
211.6232-1.0246-0.36583.06151.16963.52890.1036-1.10570.86460.9822-0.0845-0.3668-0.60370.10280.13010.709-0.1536-0.16350.8504-0.32810.660522.384229.27125.6605
220.0153-0.1032-0.01520.64870.66076.7177-0.0718-0.64090.75710.291-0.4209-0.2391-0.30280.04680.40580.4764-0.1208-0.12910.5618-0.2410.588425.244828.930816.0666
239.35784.92184.35934.8043.02838.9902-0.0785-0.2960.45940.0232-0.0157-0.3882-0.32610.40370.07610.2519-0.00010.00850.3544-0.0350.414329.634424.14677.658
242.5093-0.05630.05362.373-0.94040.50780.2395-0.447-0.14060.0605-0.2038-0.15180.02910.1296-0.04220.2375-0.0233-0.02180.268-0.02190.187518.386211.5258.2909
252.6953-0.4450.10743.9129-0.5473.0620.0736-1.06590.28010.5744-0.04560.1018-0.3549-0.1709-0.00540.3738-0.12760.00160.64-0.09890.31947.584114.956721.915
265.98231.3455-1.05442.3159-0.21283.5543-0.0803-0.5161-0.2830.3011-0.044-0.0712-0.111-0.04580.12350.36780.0209-0.05880.27320.11240.335110.2176-3.614914.9361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 227 )
3X-RAY DIFFRACTION3chain 'A' and (resid 228 through 252 )
4X-RAY DIFFRACTION4chain 'A' and (resid 253 through 329 )
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 441 )
6X-RAY DIFFRACTION6chain 'A' and (resid 442 through 481 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 24 )
8X-RAY DIFFRACTION8chain 'B' and (resid 25 through 75 )
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 288 )
10X-RAY DIFFRACTION10chain 'B' and (resid 289 through 363 )
11X-RAY DIFFRACTION11chain 'B' and (resid 364 through 440 )
12X-RAY DIFFRACTION12chain 'B' and (resid 441 through 481 )
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 24 )
14X-RAY DIFFRACTION14chain 'C' and (resid 25 through 227 )
15X-RAY DIFFRACTION15chain 'C' and (resid 228 through 278 )
16X-RAY DIFFRACTION16chain 'C' and (resid 279 through 351 )
17X-RAY DIFFRACTION17chain 'C' and (resid 352 through 441 )
18X-RAY DIFFRACTION18chain 'C' and (resid 442 through 481 )
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 24 )
20X-RAY DIFFRACTION20chain 'D' and (resid 25 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 287 )
24X-RAY DIFFRACTION24chain 'D' and (resid 288 through 351 )
25X-RAY DIFFRACTION25chain 'D' and (resid 352 through 441 )
26X-RAY DIFFRACTION26chain 'D' and (resid 442 through 481 )

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