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- PDB-7pji: Crystal structure of Pseudomonas aeruginosa guaB (IMP dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 7pji
TitleCrystal structure of Pseudomonas aeruginosa guaB (IMP dehydrogenase) bound to ATP and GDP at 1.65A resolution
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMP dehydrogenase / guaB
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / ATP 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-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / INOSINIC ACID / : / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFernandez-Justel, D. / Buey, R.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-109671GB-I00 Spain
Citation
Journal: Protein Sci. / Year: 2022
Title: Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase.
Authors: Fernandez-Justel, D. / Marcos-Alcalde, I. / Abascal, F. / Vidana, N. / Gomez-Puertas, P. / Jimenez, A. / Revuelta, J.L. / Buey, R.M.
#1: Journal: Plant Physiol. / Year: 2021
Title: Unexpected diversity of ferredoxin-dependent thioredoxin reductases in cyanobacteria.
Authors: Buey, R.M. / Fernandez-Justel, D. / Gonzalez-Holgado, G. / Martinez-Julvez, M. / Gonzalez-Lopez, A. / Velazquez-Campoy, A. / Medina, M. / Buchanan, B.B. / Balsera, M.
History
DepositionAug 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,05916
Polymers104,0992
Non-polymers2,96014
Water11,638646
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

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)428,23864
Polymers416,3978
Non-polymers11,84156
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_444x-1/2,y-1/2,z-1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation7_544-y+1/2,x-1/2,z-1/21
crystal symmetry operation8_454y-1/2,-x+1/2,z-1/21
Buried area62850 Å2
ΔGint-446 kcal/mol
Surface area123540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.947, 120.947, 145.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 52049.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: guaB, CAZ10_17565, CGU42_10690, CSB93_2499, DT376_00630, DY940_09800, DZ962_03005, E4V10_03770, ECC04_008545, F7O94_09425, H2O03_23015, HW05_11140, IPC1164_08420, IPC116_03070, IPC1295_13460, ...Gene: guaB, CAZ10_17565, CGU42_10690, CSB93_2499, DT376_00630, DY940_09800, DZ962_03005, E4V10_03770, ECC04_008545, F7O94_09425, H2O03_23015, HW05_11140, IPC1164_08420, IPC116_03070, IPC1295_13460, IPC1298_02025, IPC1323_03035, IPC1481_30840, IPC1505_09885, IPC1509_02385, IPC151_02390, IPC36_21115, IPC582_15390, IPC620_11170, IPC737_18950, IPC90_16110, NCTC12924_06429, NCTC13621_00582, NCTC13628_01024, PA52Ts2_5150, PAMH19_1311, RW109_RW109_02018
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069Q6I8, IMP dehydrogenase

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Non-polymers , 7 types, 660 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Condition D11 of the commercial screening Morpheus (Gorrec, 2009): 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate ...Details: Condition D11 of the commercial screening Morpheus (Gorrec, 2009): 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 in 0.1M of the buffer system Tris (base), bicine, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.000008 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000008 Å / Relative weight: 1
ReflectionResolution: 1.65→50.7 Å / Num. obs: 84861 / % possible obs: 67.8 % / Redundancy: 13.9 % / Biso Wilson estimate: 25.18 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.025 / Rrim(I) all: 0.094 / Net I/σ(I): 13.18
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.76 / Mean I/σ(I) obs: 0.39 / Num. unique obs: 4228 / CC1/2: 0.287 / CC star: 0.668 / Rpim(I) all: 0.489 / Rrim(I) all: 1.827 / % possible all: 7.09

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Processing

Software
NameVersionClassification
PHENIXdev_3689refinement
PHENIXdev_3689refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AVF

4avf


Resolution: 1.65→50.7 Å / SU ML: 0.1407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.44
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1953 4286 5.06 %
Rwork0.1723 80342 -
obs0.1734 84628 67.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.28 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 184 647 7247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00686693
X-RAY DIFFRACTIONf_angle_d1.04599100
X-RAY DIFFRACTIONf_chiral_restr0.05791092
X-RAY DIFFRACTIONf_plane_restr0.0061142
X-RAY DIFFRACTIONf_dihedral_angle_d17.43682406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.316640.246540X-RAY DIFFRACTION1.09
1.67-1.690.3808100.2264205X-RAY DIFFRACTION5.13
1.69-1.710.214300.2602591X-RAY DIFFRACTION15.03
1.71-1.730.3249610.26841015X-RAY DIFFRACTION25.88
1.73-1.750.3049620.2441183X-RAY DIFFRACTION29.9
1.75-1.780.3363610.23711438X-RAY DIFFRACTION35.94
1.78-1.80.2514800.24071512X-RAY DIFFRACTION38.86
1.8-1.830.2415860.23631691X-RAY DIFFRACTION43.11
1.83-1.860.24111140.22631861X-RAY DIFFRACTION47.07
1.86-1.890.27431060.2251976X-RAY DIFFRACTION50.76
1.89-1.920.22011250.22182155X-RAY DIFFRACTION55.09
1.92-1.960.22721110.22512330X-RAY DIFFRACTION58.82
1.96-20.25391170.21152511X-RAY DIFFRACTION63.23
2-2.040.23191560.19642748X-RAY DIFFRACTION69.64
2.04-2.080.22681800.19352897X-RAY DIFFRACTION73.79
2.08-2.130.24231500.18753079X-RAY DIFFRACTION77.88
2.13-2.180.2391710.18123169X-RAY DIFFRACTION80.77
2.18-2.240.24031700.1843339X-RAY DIFFRACTION83.97
2.24-2.310.19171690.1813451X-RAY DIFFRACTION87.55
2.31-2.380.20771990.17753642X-RAY DIFFRACTION91.71
2.38-2.470.21012000.18063826X-RAY DIFFRACTION96.92
2.47-2.570.19682230.18183922X-RAY DIFFRACTION100
2.57-2.680.1981990.17793986X-RAY DIFFRACTION100
2.68-2.820.21412170.17553931X-RAY DIFFRACTION100
2.82-30.20562350.183949X-RAY DIFFRACTION99.98
3-3.230.20752080.17393947X-RAY DIFFRACTION100
3.23-3.560.18762270.15863963X-RAY DIFFRACTION100
3.56-4.070.15732200.14423938X-RAY DIFFRACTION100
4.07-5.130.14242170.13513998X-RAY DIFFRACTION99.98
5.13-50.70.20151780.18684049X-RAY DIFFRACTION99.79

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