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- PDB-6mgu: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

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Basic information

Entry
Database: PDB / ID: 6mgu
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus Anthracis in the complex with inhibitor Oxanosine monophosphate
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 / GMP 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
Chem-JQS / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKim, Y. / Maltseva, N. / Yu, R. / Hedstrom, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus Anthracis in the complex with inhibitor Oxanosine monophosphate
Authors: Kim, Y. / Maltseva, N. / Yu, R. / Hedstrom, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)77,98513
Polymers76,4762
Non-polymers1,50911
Water4,252236
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)156,27128
Polymers152,9524
Non-polymers3,31924
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 area23740 Å2
ΔGint-63 kcal/mol
Surface area46360 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)155,67024
Polymers152,9524
Non-polymers2,71920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area22450 Å2
ΔGint-75 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.411, 86.411, 90.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38237.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium)
Gene: guaB, BA_0008, A9486_01210, ABW01_29210, BVG01_30935, COL95_27530
Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0J1HJU0, UniProt: A0A6L8P2U9*PLUS, IMP dehydrogenase

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Non-polymers , 6 types, 247 molecules

#2: Chemical ChemComp-JQS / 5-[(Z)-(aminomethylidene)amino]-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid


Mass: 366.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N4O9P
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Magnesium Chloride, 0.1 M MES:NaOH pH 6.5, 30% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 97222 / % possible obs: 98.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.56 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.6
Reflection shellResolution: 1.54→1.57 Å / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 0.7 / Num. unique all: 4080 / CC1/2: 0.4 / % possible all: 82.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→43.206 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 20.52
RfactorNum. reflection% reflection
Rfree0.1977 4781 4.93 %
Rwork0.1645 --
obs0.1662 97075 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.2 Å2
Refinement stepCycle: LAST / Resolution: 1.54→43.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 96 236 5424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065362
X-RAY DIFFRACTIONf_angle_d1.0067253
X-RAY DIFFRACTIONf_dihedral_angle_d20.6991982
X-RAY DIFFRACTIONf_chiral_restr0.364846
X-RAY DIFFRACTIONf_plane_restr0.005940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.55750.38271390.32952499X-RAY DIFFRACTION81
1.5575-1.57590.32121130.29412909X-RAY DIFFRACTION92
1.5759-1.59510.30521770.25433010X-RAY DIFFRACTION98
1.5951-1.61530.27981410.23593080X-RAY DIFFRACTION98
1.6153-1.63650.26341550.21993127X-RAY DIFFRACTION99
1.6365-1.6590.23961410.2123042X-RAY DIFFRACTION98
1.659-1.68270.21371640.20423068X-RAY DIFFRACTION99
1.6827-1.70780.25641610.19853068X-RAY DIFFRACTION99
1.7078-1.73450.24281400.19433133X-RAY DIFFRACTION99
1.7345-1.76290.24831870.18673061X-RAY DIFFRACTION99
1.7629-1.79330.22111690.18583086X-RAY DIFFRACTION99
1.7933-1.82590.22831750.17993031X-RAY DIFFRACTION99
1.8259-1.8610.20181330.16713111X-RAY DIFFRACTION99
1.861-1.8990.21331680.15943110X-RAY DIFFRACTION99
1.899-1.94030.19481480.1513095X-RAY DIFFRACTION99
1.9403-1.98540.1791630.15223075X-RAY DIFFRACTION100
1.9854-2.03510.19071620.15883145X-RAY DIFFRACTION100
2.0351-2.09010.19161320.15883142X-RAY DIFFRACTION100
2.0901-2.15160.18721600.15673096X-RAY DIFFRACTION100
2.1516-2.22110.21091380.16043150X-RAY DIFFRACTION99
2.2211-2.30040.19221640.15723090X-RAY DIFFRACTION100
2.3004-2.39250.19091850.15463116X-RAY DIFFRACTION100
2.3925-2.50140.18051540.16313109X-RAY DIFFRACTION100
2.5014-2.63330.18421510.16383143X-RAY DIFFRACTION100
2.6333-2.79820.22242000.17643096X-RAY DIFFRACTION99
2.7982-3.01420.22681590.18223128X-RAY DIFFRACTION100
3.0142-3.31750.21111640.18353148X-RAY DIFFRACTION100
3.3175-3.79730.18091910.16363121X-RAY DIFFRACTION100
3.7973-4.78320.15481680.13443126X-RAY DIFFRACTION99
4.7832-43.22250.20821790.15613179X-RAY DIFFRACTION99

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