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- PDB-4q32: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 4q32
TitleCrystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and C91
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / dehydrogenase
Function / homology
Function and homology information


IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / 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 ...IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / 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-C91 / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.788 Å
AuthorsMaltseva, N. / Kim, Y. / Makowska-Grzyska, M. / Mulligan, R. / Gu, M. / Zhang, M. / Mandapati, K. / Gollapalli, D.R. / Gorla, S.K. / Hedstrom, L. ...Maltseva, N. / Kim, Y. / Makowska-Grzyska, M. / Mulligan, R. / Gu, M. / Zhang, M. / Mandapati, K. / Gollapalli, D.R. / Gorla, S.K. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / 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 C91
Authors: Maltseva, N. / Kim, Y. / Makowska-Grzyska, M. / Mulligan, R. / Gu, M. / Zhang, M. / Mandapati, K. / Gollapalli, D.R. / Gorla, S.K. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Sep 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)156,67212
Polymers153,7654
Non-polymers2,9078
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20950 Å2
ΔGint-125 kcal/mol
Surface area46970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.611, 77.611, 222.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 38441.266 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / NCTC 8237 / Type A / Gene: CPF_2558, guaB / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: Q0TN42, UniProt: A0A0H2YRZ7*PLUS, IMP dehydrogenase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-C91 / N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide


Mass: 378.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H18N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CBS DOMAIN (UNP RESIDUES 89-215 HAS BEEN REPLACED WITH A SER-GLY-GLY LINKER.

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1% ammmonium acetate, 0.1 M Bis-Tris, pH 5.5, 17% PEG10000, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2012 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.788→50 Å / Num. all: 32619 / Num. obs: 32619 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 64.8 Å2 / Rsym value: 0.104 / Net I/σ(I): 9.4
Reflection shellResolution: 2.788→2.85 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1635 / Rsym value: 0.704 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1593)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TSD

3tsd


Resolution: 2.788→34.709 Å / SU ML: 0.37 / Isotropic thermal model: MIXED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1652 5.08 %RANDOM
Rwork0.173 ---
all0.176 32537 --
obs0.176 32537 99.43 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.2 Å2
Refinement stepCycle: LAST / Resolution: 2.788→34.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9985 0 208 81 10274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310404
X-RAY DIFFRACTIONf_angle_d0.68614072
X-RAY DIFFRACTIONf_dihedral_angle_d13.6753873
X-RAY DIFFRACTIONf_chiral_restr0.0241622
X-RAY DIFFRACTIONf_plane_restr0.0031799
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.788-2.86970.32981400.25492498263896
2.8697-2.96230.3411370.244925772714100
2.9623-3.06810.33491370.234525782715100
3.0681-3.19080.29441310.215125852716100
3.1908-3.3360.25991420.206825632705100
3.336-3.51170.28191250.192226192744100
3.5117-3.73150.23671390.183625642703100
3.7315-4.01920.2081330.167925902723100
4.0192-4.42290.2021500.149225782728100
4.4229-5.06120.19651230.135825792702100
5.0612-6.37020.20021660.165225852751100
6.3702-34.71140.1721290.1552569269898
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)
11.6512-0.2322-0.62560.66290.87474.35420.0584-0.16950.13490.29050.0091-0.1791-0.12130.2353-0.0770.4917-0.0164-0.0910.3764-0.01750.60643.19623.490622.2723
23.1148-0.60330.77541.1333-1.22855.1182-0.0701-0.33550.62180.305-0.0467-0.2851-0.6430.38740.25030.6073-0.0984-0.18960.4407-0.10030.730540.57940.585129.2735
33.60030.1429-0.62121.0981-0.54362.2364-0.0468-0.0919-0.04280.048-0.0467-0.06960.05890.07730.07280.44710.0214-0.09550.3376-0.02510.505332.184625.654721.113
41.17130.1993-0.48161.9494-0.19236.0808-0.14850.0317-0.1237-0.2488-0.1087-0.18280.27680.08070.18630.44870.11940.02580.38350.01340.567340.438212.166912.7063
53.79293.67323.21368.73426.62035.24330.4222-0.11730.01370.05620.0806-0.6324-0.09970.3529-0.12120.43360.07580.04330.43740.06950.366831.76467.4715-13.5555
62.66680.12270.97393.4919-0.21754.56610.1377-0.1305-0.35870.25570.1769-0.16960.61150.0744-0.22680.73730.2102-0.0050.5273-0.04020.628243.4893-15.371-1.2844
71.3903-1.6691-0.46354.3675-2.37683.8741-0.0198-0.31970.0358-0.12490.1771-0.96890.64590.7465-0.11990.61310.3274-0.08670.8583-0.00380.648954.2589-10.79434.4957
84.0008-1.7561-1.14892.46621.15893.64330.00830.18920.10490.01060.0549-0.3839-0.14170.4804-0.02860.38080.0212-0.00150.4540.00310.492150.78062.5865-1.8195
94.86932.1953-2.00393.3796-1.05396.74250.1811-0.2543-0.45580.3701-0.2885-0.3789-0.25460.35360.13910.51660.0684-0.0820.41580.060.376637.6586-1.4728-6.8868
103.79071.4570.64525.41312.00463.54750.1712-0.4291-0.63060.821-0.52930.03331.1468-0.16610.23781.04110.02630.10820.71740.12830.579631.5247-10.612112.1989
113.38840.06130.63571.7292-0.02531.68930.03330.3314-0.0594-0.061-0.07610.1410.15720.07050.0670.54740.1070.08080.4082-0.0370.421730.3015-2.5849-7.3394
125.2206-0.2110.50726.7615-0.42251.55610.2812-0.65430.2650.72940.27530.3986-0.32130.2757-0.44070.88990.02880.0460.7028-0.01430.487613.9883-2.5812-2.9581
134.0121-1.0720.0931.3150.02821.9055-0.26640.07960.45670.1569-0.00970.0335-0.2465-0.07680.24220.5399-0.0452-0.07790.3129-0.03040.541111.004442.61526.7226
142.7562-1.121-0.38432.63230.7631.0965-0.0764-0.04320.3439-0.2537-0.08930.2567-0.2571-0.18620.17390.48280.0224-0.11480.3546-0.01970.5176-1.429743.1897-4.9244
152.21720.28130.66832.62910.18391.6848-0.0525-0.1875-0.03160.2823-0.0037-0.0374-0.0768-0.07240.07370.50880.01-0.0180.4234-0.01260.45489.215332.59759.817
160.74561.65920.40033.9550.51821.06210.10490.0984-0.15010.0116-0.16650.03760.10080.04210.05760.35930.0565-0.020.4235-0.01310.35283.616310.7893-21.3201
176.58571.11241.15214.8439-0.49354.2459-0.06960.1051-0.7774-0.35830.20910.55070.2624-0.2397-0.18790.647-0.0166-0.11750.5335-0.160.6148-1.1411-7.4005-28.5348
186.28811.4989-2.33553.6025-1.01770.9508-0.10310.317-0.4607-0.2923-0.0721-0.00360.16820.19240.25370.50470.05660.01280.55690.00550.34478.1239-5.5572-31.5753
193.33450.83140.91341.21341.11054.5126-0.15790.41770.016-0.4378-0.05350.05650.0420.23940.20740.47750.08960.05690.49010.01820.428317.0734.7395-27.8048
204.00231.716-2.47434.4163-2.27553.4018-0.21250.09950.04790.43950.0649-0.03230.0876-0.18220.15630.3983-0.0053-0.07130.3815-0.01950.40023.34435.9096-12.4416
213.4143-0.28390.23876.5301-0.7661.67330.1259-0.0389-0.20580.0364-0.24670.46960.1907-0.00720.09760.3655-0.0478-0.01660.3823-0.05880.21842.45595.7318-11.8755
222.9714-0.5693-0.19531.67271.89942.5467-0.0239-0.23930.04770.3159-0.06040.08530.16210.26450.09870.5925-0.0132-0.05460.31970.04570.6487.442522.568-8.8679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 298 )
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 357 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 88 )
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 129 through 205 )
9X-RAY DIFFRACTION9chain 'B' and (resid 206 through 234 )
10X-RAY DIFFRACTION10chain 'B' and (resid 235 through 270 )
11X-RAY DIFFRACTION11chain 'B' and (resid 271 through 342 )
12X-RAY DIFFRACTION12chain 'B' and (resid 343 through 357 )
13X-RAY DIFFRACTION13chain 'C' and (resid 4 through 63 )
14X-RAY DIFFRACTION14chain 'C' and (resid 64 through 205 )
15X-RAY DIFFRACTION15chain 'C' and (resid 206 through 357 )
16X-RAY DIFFRACTION16chain 'D' and (resid 4 through 75 )
17X-RAY DIFFRACTION17chain 'D' and (resid 76 through 103 )
18X-RAY DIFFRACTION18chain 'D' and (resid 104 through 128 )
19X-RAY DIFFRACTION19chain 'D' and (resid 129 through 205 )
20X-RAY DIFFRACTION20chain 'D' and (resid 206 through 260 )
21X-RAY DIFFRACTION21chain 'D' and (resid 261 through 316 )
22X-RAY DIFFRACTION22chain 'D' and (resid 317 through 357 )

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