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

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Basic information

Entry
Database: PDB / ID: 5uzc
TitleCrystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P221
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 / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS 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 / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / 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-8N1 / ACETIC ACID / FORMIC ACID / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 P221
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 1.1Oct 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)157,80721
Polymers153,7654
Non-polymers4,04217
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23320 Å2
ΔGint-189 kcal/mol
Surface area46450 Å2
2
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules

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)315,61342
Polymers307,5308
Non-polymers8,08334
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area50110 Å2
ΔGint-383 kcal/mol
Surface area89440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.017, 119.305, 97.199
Angle α, β, γ (deg.)90.00, 102.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-718-

HOH

21A-722-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#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 (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 , 7 types, 426 molecules

#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-8N1 / N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-xylofuranosylamine


Mass: 475.965 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30ClN3O5
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M ammonium acetate, 0.1M Tris pH 8.5, 45% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2016 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 120850 / % possible obs: 99.3 % / Redundancy: 5 % / Biso Wilson estimate: 34.84 Å2 / Rsym value: 0.107 / Net I/σ(I): 15.05
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5984 / CC1/2: 0.67 / Rsym value: 0.797 / % possible all: 98.1

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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: 4Q32

4q32


Resolution: 1.85→44.513 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.08
RfactorNum. reflection% reflection
Rfree0.2007 5934 4.91 %
Rwork0.1708 --
obs0.1723 120807 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10143 0 274 409 10826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110805
X-RAY DIFFRACTIONf_angle_d1.20814643
X-RAY DIFFRACTIONf_dihedral_angle_d23.2174022
X-RAY DIFFRACTIONf_chiral_restr0.0731689
X-RAY DIFFRACTIONf_plane_restr0.0061866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.846-1.86690.34582000.32063609X-RAY DIFFRACTION93
1.8669-1.88890.31511850.30423749X-RAY DIFFRACTION99
1.8889-1.91190.33231990.28023833X-RAY DIFFRACTION99
1.9119-1.93610.29971940.27863831X-RAY DIFFRACTION99
1.9361-1.96160.27261810.25373844X-RAY DIFFRACTION99
1.9616-1.98850.2591850.24273845X-RAY DIFFRACTION99
1.9885-2.01690.25852180.23513772X-RAY DIFFRACTION99
2.0169-2.0470.25931910.22833767X-RAY DIFFRACTION98
2.047-2.0790.25712050.21293868X-RAY DIFFRACTION99
2.079-2.11310.25062050.20573818X-RAY DIFFRACTION100
2.1131-2.14950.23281830.20263822X-RAY DIFFRACTION100
2.1495-2.18860.21451970.19133885X-RAY DIFFRACTION100
2.1886-2.23070.22831950.18883801X-RAY DIFFRACTION100
2.2307-2.27620.22351920.17673861X-RAY DIFFRACTION99
2.2762-2.32570.2132010.18183835X-RAY DIFFRACTION100
2.3257-2.37980.19261940.1783866X-RAY DIFFRACTION99
2.3798-2.43930.20912150.17633819X-RAY DIFFRACTION99
2.4393-2.50530.20222120.17193762X-RAY DIFFRACTION98
2.5053-2.5790.21281890.17083859X-RAY DIFFRACTION100
2.579-2.66220.20492170.16953841X-RAY DIFFRACTION100
2.6622-2.75740.18551940.17823830X-RAY DIFFRACTION100
2.7574-2.86770.21162030.17733832X-RAY DIFFRACTION100
2.8677-2.99820.21722020.18093900X-RAY DIFFRACTION100
2.9982-3.15630.18932040.17373808X-RAY DIFFRACTION99
3.1563-3.3540.21681890.17123850X-RAY DIFFRACTION99
3.354-3.61280.1852300.15943823X-RAY DIFFRACTION100
3.6128-3.97620.16881990.1483868X-RAY DIFFRACTION100
3.9762-4.5510.1661600.13613897X-RAY DIFFRACTION99
4.551-5.73190.18621980.14983862X-RAY DIFFRACTION99
5.7319-44.52560.17781970.15273916X-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)
11.46060.22910.24881.5228-0.14131.35540.03510.13350.1406-0.09690.07310.1097-0.2953-0.0733-0.10930.37690.07810.02640.26380.05560.311-16.31229.117720.0885
21.25510.2535-0.43660.8726-0.76962.5851-0.03770.37890.1228-0.21250.06490.0633-0.29780.0118-0.04180.47580.11470.02010.31970.03710.3768-16.653929.176512.5303
33.2875-0.35240.66843.3527-0.17645.59340.07380.33620.2461-0.2025-0.04090.1067-0.2295-0.0217-0.06680.19930.0128-0.00880.23680.0660.2713-25.110614.535218.9674
41.4006-0.4820.46867.5564-0.69920.8911-0.082-0.0584-0.14520.18920.0070.2273-0.0759-0.10260.07670.20110.0171-0.00990.3040.00620.2732-21.7884-2.577831.2378
52.0954-0.60730.37021.6902-1.10742.3640.18960.545-0.3822-0.3426-0.11260.27680.1499-0.2034-0.08170.36130.0215-0.12290.5509-0.15770.4123-39.1725-9.7439.1552
63.00770.47110.38271.63120.37731.28770.06520.1543-0.0194-0.1314-0.12330.395-0.0161-0.39620.06030.23910.0664-0.04020.4557-0.03660.3763-42.26261.752519.1882
71.227-0.9396-0.05982.5467-0.8711.96660.19790.5424-0.1189-0.5669-0.26790.0179-0.0254-0.11230.05170.33310.0561-0.05760.4648-0.06850.2731-26.0819-5.00448.9756
83.16790.4753-0.5173.16620.42092.68940.050.1585-0.1605-0.1951-0.0217-0.0541-0.1039-0.01-0.03580.21820.0386-0.0590.25530.01170.3018-14.4569-9.499721.7287
95.14970.64361.22693.76990.20853.40140.1391-0.33-0.44060.0721-0.1382-0.0564-0.0175-0.16080.02930.2021-0.03970.01740.21090.04870.2281-0.3605-2.441537.2974
101.6950.1913-0.05331.4223-0.03960.9653-0.03150.0479-0.4252-0.0709-0.0055-0.29880.16770.09870.0390.22280.01520.00490.2444-0.010.45311.4586-23.679127.3636
113.62810.0120.09352.15671.89294.14830.09450.5353-0.5062-0.14140.0296-0.40060.1210.1925-0.1960.28840.01490.04450.19180.06710.42415.0078-15.260619.0381
123.226-0.0461-0.93733.3282-0.74752.37660.05530.1677-0.0843-0.0328-0.033-0.2213-0.2250.002-0.00190.1876-0.0622-0.04590.2373-0.0260.30047.58680.693629.7048
133.36990.6517-1.6070.2317-0.62972.8552-0.1756-0.2636-0.46890.1371-0.00540.09630.0562-0.13290.15330.281-0.00320.02960.31530.03940.2579-5.548715.638138.4632
141.26170.0785-0.22761.1745-0.06330.840.0917-0.0753-0.02560.0738-0.0655-0.2272-0.11770.1725-0.02510.2849-0.0822-0.00530.30010.00490.350319.672317.902632.9524
153.34651.14620.322.8365-0.00011.68380.02850.02310.1305-0.094-0.095-0.0744-0.1641-0.13960.05710.28170.04310.0480.1710.01310.2678-1.998324.381626.5503
160.88690.8599-0.72043.2311-0.9011.50.11940.23510.4692-0.16140.04310.2612-0.5476-0.2155-0.17720.52540.13610.04350.35240.08130.3998-22.528236.564419.0906
174.1188-2.51262.6623.1252-2.83423.36250.14170.19720.8749-0.0595-0.295-0.1206-0.4711-0.03630.17380.70580.11020.12990.27930.03910.508-15.519548.472424.7292
183.9009-2.46360.67149.2022-0.96171.80160.0522-0.27170.33020.34680.13160.2182-0.71-0.192-0.17210.60540.07340.12010.2897-0.01870.3301-16.902444.133734.2871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 289 through 384 )
2X-RAY DIFFRACTION2chain 'C' and (resid 385 through 441 )
3X-RAY DIFFRACTION3chain 'C' and (resid 442 through 481 )
4X-RAY DIFFRACTION4chain 'D' and (resid -1 through 24 )
5X-RAY DIFFRACTION5chain 'D' and (resid 25 through 88 )
6X-RAY DIFFRACTION6chain 'D' and (resid 89 through 329 )
7X-RAY DIFFRACTION7chain 'D' and (resid 330 through 440 )
8X-RAY DIFFRACTION8chain 'D' and (resid 441 through 482 )
9X-RAY DIFFRACTION9chain 'A' and (resid 2 through 24 )
10X-RAY DIFFRACTION10chain 'A' and (resid 25 through 384 )
11X-RAY DIFFRACTION11chain 'A' and (resid 385 through 440 )
12X-RAY DIFFRACTION12chain 'A' and (resid 441 through 482 )
13X-RAY DIFFRACTION13chain 'B' and (resid -2 through 24 )
14X-RAY DIFFRACTION14chain 'B' and (resid 25 through 441 )
15X-RAY DIFFRACTION15chain 'B' and (resid 442 through 482 )
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 227 )
17X-RAY DIFFRACTION17chain 'C' and (resid 228 through 252 )
18X-RAY DIFFRACTION18chain 'C' and (resid 253 through 288 )

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