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- PDB-5uqf: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

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Basic information

Entry
Database: PDB / ID: 5uqf
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with IMP and the inhibitor P225
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IMPDH / TIM barrel / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / purine nucleotide biosynthetic process
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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / 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 speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
Campylobacter jejuni subsp. jejuni CG8486 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsKim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / 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 the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with IMP and the inhibitor P225
Authors: Kim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,53332
Polymers130,5743
Non-polymers3,95929
Water1,26170
1
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,40644
Polymers174,0994
Non-polymers5,30740
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area26440 Å2
ΔGint-178 kcal/mol
Surface area49780 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,04648
Polymers174,0994
Non-polymers5,94744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area29300 Å2
ΔGint-339 kcal/mol
Surface area48950 Å2
MethodPISA
3
C: Inosine-5'-monophosphate dehydrogenase
hetero molecules

C: Inosine-5'-monophosphate dehydrogenase
hetero molecules

C: Inosine-5'-monophosphate dehydrogenase
hetero molecules

C: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,68036
Polymers174,0994
Non-polymers4,58132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area26510 Å2
ΔGint-272 kcal/mol
Surface area49850 Å2
MethodPISA
4
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)358,81288
Polymers348,1998
Non-polymers10,61380
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area61480 Å2
ΔGint-486 kcal/mol
Surface area93910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.526, 118.526, 451.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-503-

SO4

21A-604-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 43524.820 Da / Num. of mol.: 3
Mutation: the CBS domain (residues 92-195) is replaced with "Gly"
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter), (gene. exp.) Campylobacter jejuni subsp. jejuni CG8486 (Campylobacter)
Gene: guaB, CJ14980A_1064, guaB, Cj8486_1016 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic
References: UniProt: A0A1B3XFT6, UniProt: A5KFK9, IMP dehydrogenase

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Non-polymers , 8 types, 99 molecules

#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: C21H23ClN2O4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 1.2 M sodium dihydrogen phosphate, 0.8 M potassium hydrogen phosphate, 0.1 M CAPS pH 10.5, 0.2 M lithium sulfate

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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: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 43356 / % possible obs: 99.3 % / Redundancy: 4.3 % / Rsym value: 0.137 / Net I/σ(I): 10.7
Reflection shellResolution: 2.73→2.78 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.48 / Num. unique obs: 2145 / CC1/2: 0.696 / Rsym value: 0.757 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R7J

4r7j


Resolution: 2.73→46.55 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.74
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 2092 4.84 %random
Rwork0.1746 ---
obs0.1772 43204 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.6 Å2
Refinement stepCycle: LAST / Resolution: 2.73→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7908 0 244 70 8222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088252
X-RAY DIFFRACTIONf_angle_d1.07911132
X-RAY DIFFRACTIONf_dihedral_angle_d22.9813045
X-RAY DIFFRACTIONf_chiral_restr0.0621287
X-RAY DIFFRACTIONf_plane_restr0.0061400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7239-2.78730.31221330.25062651X-RAY DIFFRACTION96
2.7873-2.8570.27261360.21942677X-RAY DIFFRACTION99
2.857-2.93420.26331250.21882733X-RAY DIFFRACTION99
2.9342-3.02060.3021370.22372680X-RAY DIFFRACTION99
3.0206-3.1180.33121660.22562727X-RAY DIFFRACTION100
3.118-3.22950.27731350.20692677X-RAY DIFFRACTION99
3.2295-3.35870.25481410.19322722X-RAY DIFFRACTION99
3.3587-3.51150.251320.18532715X-RAY DIFFRACTION99
3.5115-3.69660.25491480.17292737X-RAY DIFFRACTION99
3.6966-3.92810.23191380.15782737X-RAY DIFFRACTION99
3.9281-4.23120.17291400.13852770X-RAY DIFFRACTION100
4.2312-4.65660.18261290.12922788X-RAY DIFFRACTION100
4.6566-5.32960.17581420.13512791X-RAY DIFFRACTION100
5.3296-6.71160.22661460.18192843X-RAY DIFFRACTION100
6.7116-46.55690.19791440.18232864X-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)
14.88960.65971.78651.90281.00911.94240.508-0.11860.00480.0993-0.15910.1233-0.1022-0.1162-0.32320.40970.01430.07920.45350.08370.2919-15.441412.837133.3846
23.84550.58270.35674.8567-1.0894.13910.1310.12470.1828-0.02090.06270.0685-0.3657-0.118-0.17110.3150.04990.06760.2513-0.00240.3429-15.674537.133319.467
31.0606-0.48930.10071.56980.59070.31960.0387-0.19190.21530.13620.0059-0.0031-0.0551-0.092-0.04740.325-0.01020.07270.3717-0.03950.3413-5.449630.108930.3276
41.95120.6171-0.46960.5853-0.0632.46-0.04820.2855-0.1074-0.09790.0719-0.00910.0022-0.0513-0.02760.32440.02530.01130.22860.0010.347-9.915722.268511.7743
51.6316-0.78530.78913.09832.34474.92020.23140.17270.0670.2735-0.1275-0.25720.3306-0.145-0.17610.3229-0.05010.04620.290.1050.3893-17.31268.087824.9555
61.01740.048-0.41261.4454-0.17281.9208-0.0014-0.2275-0.03380.27340.0924-0.06290.01510.1026-0.10040.3205-0.0192-0.04470.3112-0.0270.2475-39.318844.2076104.7365
72.25292.97941.18965.1150.08632.7125-0.01930.1749-0.3627-0.34850.0720.04880.39370.0154-0.03870.32690.0409-0.02590.3597-0.01150.3187-40.258228.11587.8908
82.56222.7452-0.49335.0130.15213.1963-0.0046-0.2221-0.095-0.42680.0515-0.38990.05250.4984-0.08570.38920.1125-0.05010.3837-0.04130.4118-34.11522.378891.5222
96.17-1.1609-2.91161.51291.14763.87520.28820.246-0.3813-0.1288-0.2678-0.04180.2497-0.38770.00240.3611-0.031-0.08920.29850.03290.2883-46.344319.606798.5065
101.32320.1211-0.3781.12590.36480.24610.0398-0.1472-0.04870.06320.0283-0.06350.04430.0947-0.04870.28310.0263-0.03180.28950.00090.2357-48.22833.2809104.7691
115.4163-0.5198-0.67542.0177-2.68527.120.09280.00360.0612-0.3696-0.1345-0.14140.59750.2590.05540.31320.01160.010.2663-0.07610.2698-48.238836.686679.6404
122.91930.3047-0.57451.37260.42013.5447-0.25040.3875-0.0936-0.3560.1629-0.0871-0.08690.34980.0240.29020.0625-0.01650.1620.05420.2975-42.223341.528689.2724
132.9624-1.238-0.99144.0329-1.10982.86230.02340.20790.0224-0.04180.0194-0.036-0.0945-0.1722-0.06510.2756-0.0707-0.03720.284-0.05320.3086-40.603254.910797.5577
142.3897-0.15270.60041.6415-0.08811.06870.01290.1932-0.2086-0.24220.09040.07420.14860.0981-0.12610.3861-0.0442-0.05520.32570.01390.2896-71.147336.353443.0688
157.325-0.4178-1.00095.3886-0.28794.5655-0.0426-0.2788-0.31510.15940.08420.06490.3139-0.2391-0.04920.3657-0.0165-0.05630.21940.00420.3854-68.696617.980654.9435
161.98240.65090.06980.4274-0.23470.8697-0.04910.1795-0.19-0.2780.1394-0.11780.10770.0577-0.09590.3554-0.0149-0.03290.3224-0.06980.4024-59.875528.65442.2594
176.70672.1902-3.3412.60940.39914.1101-0.0838-0.1918-0.290.2824-0.0107-0.08550.22930.18510.10960.33260.0252-0.04120.33810.04330.2897-59.101834.617565.0603
183.07530.1927-0.2993.3409-1.6744.14020.01340.26160.0577-0.25660.10350.36280.2296-0.2884-0.17040.26560.0177-0.02160.3063-0.03890.3698-77.116442.464244.0383
195.00772.6423-2.57163.94382.54357.2746-0.3194-0.21820.19510.40160.0218-0.6014-0.20420.25450.24740.43230.0408-0.06890.44820.13430.4078-75.237952.26160.3277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 226 )
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 361 )
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 441 )
5X-RAY DIFFRACTION5chain 'A' and (resid 442 through 482 )
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 45 )
7X-RAY DIFFRACTION7chain 'B' and (resid 46 through 74 )
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 226 )
9X-RAY DIFFRACTION9chain 'B' and (resid 227 through 250 )
10X-RAY DIFFRACTION10chain 'B' and (resid 251 through 356 )
11X-RAY DIFFRACTION11chain 'B' and (resid 357 through 391 )
12X-RAY DIFFRACTION12chain 'B' and (resid 392 through 441 )
13X-RAY DIFFRACTION13chain 'B' and (resid 442 through 482 )
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 53 )
15X-RAY DIFFRACTION15chain 'C' and (resid 54 through 226 )
16X-RAY DIFFRACTION16chain 'C' and (resid 227 through 361 )
17X-RAY DIFFRACTION17chain 'C' and (resid 362 through 422 )
18X-RAY DIFFRACTION18chain 'C' and (resid 423 through 466 )
19X-RAY DIFFRACTION19chain 'C' and (resid 467 through 482 )

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