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

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Basic information

Entry
Database: PDB / ID: 5upy
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Listeria Monocytogenes in the complex with IMP and Q21
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMPDH / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
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
INOSINIC ACID / Chem-Q21 / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Osipiuk, J. / 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 Listeria Monocytogenes in the complex with IMP and Q21
Authors: Kim, Y. / Makowska-Grzyska, M. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,71210
Polymers38,4561
Non-polymers1,2569
Water1,874104
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)158,84640
Polymers153,8244
Non-polymers5,02236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation20_555x,-z,y1
Buried area29140 Å2
ΔGint-155 kcal/mol
Surface area46260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.165, 174.165, 174.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 38455.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: guaB / Plasmid: pMCSG50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q926Y9, IMP dehydrogenase

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Non-polymers , 6 types, 113 molecules

#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-Q21 / (2S)-2-(naphthalen-1-yloxy)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]propanamide


Mass: 409.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H19N3O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 10% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 19178 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 12.7
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.4 % / Num. unique obs: 939 / CC1/2: 0.702 / Rsym value: 0.759 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2411: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MY8

4my8


Resolution: 2.35→43.541 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.23
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 985 5.14 %random
Rwork0.1636 ---
obs0.1659 19157 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→43.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 85 104 2771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042713
X-RAY DIFFRACTIONf_angle_d0.7083663
X-RAY DIFFRACTIONf_dihedral_angle_d18.4981600
X-RAY DIFFRACTIONf_chiral_restr0.047420
X-RAY DIFFRACTIONf_plane_restr0.004467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.345-2.46870.2651250.21552558X-RAY DIFFRACTION99
2.4687-2.62330.22591510.20392522X-RAY DIFFRACTION100
2.6233-2.82580.25481410.19232560X-RAY DIFFRACTION100
2.8258-3.11010.22341490.18232564X-RAY DIFFRACTION100
3.1101-3.560.21921580.16782579X-RAY DIFFRACTION100
3.56-4.48450.18111420.13752619X-RAY DIFFRACTION100
4.4845-43.54870.17751190.14242770X-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)
10.6866-0.0117-0.05991.09240.29640.8404-0.0025-0.01520.07740.0764-0.00220.0092-0.1054-0.03380.00090.20290.0153-0.00960.19810.00020.162567.040120.402523.049
27.4641.4868-1.16992.6439-2.81836.23250.10310.29920.1669-0.34350.3610.88110.2865-0.9124-0.40540.3306-0.0289-0.02160.4006-0.01260.411846.039817.817818.3775
33.4084-0.6792-0.36811.0476-1.56543.22930.099-0.0217-0.19860.12410.04420.325-0.0198-0.2189-0.12150.2661-0.05160.00440.1535-0.09570.219555.530110.729421.7248
41.86550.92570.52662.24961.13983.1847-0.0426-0.04350.0389-0.1712-0.05780.2646-0.0342-0.31080.11620.32570.0348-0.02220.2540.00940.289363.8328-2.214718.5501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 363 )
2X-RAY DIFFRACTION2chain 'A' and (resid 364 through 399 )
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 446 )
4X-RAY DIFFRACTION4chain 'A' and (resid 447 through 486 )

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