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- PDB-7r50: Crystal structure of GMP reductase from mycobacterium smegmatis i... -

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Basic information

Entry
Database: PDB / ID: 7r50
TitleCrystal structure of GMP reductase from mycobacterium smegmatis in complex with GMP.
ComponentsInosine-5-monophosphate dehydrogenase guaB1
KeywordsOXIDOREDUCTASE / GMP reductase GMPR oxidoreductase GuaB1 octamer CBS domain Bateman domain Mycobacterium smegmatis
Function / homology
Function and homology information


IMP dehydrogenase activity / purine nucleotide biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
GMP reductase-like / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Inosine-5-monophosphate dehydrogenase guaB1
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDolezal, M. / Klima, M. / Pichova, I.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/16_019/000729 Czech Republic
CitationJournal: Febs J. / Year: 2022
Title: The mycobacterial guaB1 gene encodes a guanosine 5'-monophosphate reductase with a cystathionine-beta-synthase domain.
Authors: Knejzlik, Z. / Dolezal, M. / Herkommerova, K. / Clarova, K. / Klima, M. / Dedola, M. / Zbornikova, E. / Rejman, D. / Pichova, I.
History
DepositionFeb 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

Downloads & links

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Assembly

Deposited unit
A: Inosine-5-monophosphate dehydrogenase guaB1
B: Inosine-5-monophosphate dehydrogenase guaB1
C: Inosine-5-monophosphate dehydrogenase guaB1
D: Inosine-5-monophosphate dehydrogenase guaB1
E: Inosine-5-monophosphate dehydrogenase guaB1
F: Inosine-5-monophosphate dehydrogenase guaB1
G: Inosine-5-monophosphate dehydrogenase guaB1
H: Inosine-5-monophosphate dehydrogenase guaB1
I: Inosine-5-monophosphate dehydrogenase guaB1
J: Inosine-5-monophosphate dehydrogenase guaB1
K: Inosine-5-monophosphate dehydrogenase guaB1
L: Inosine-5-monophosphate dehydrogenase guaB1
M: Inosine-5-monophosphate dehydrogenase guaB1
N: Inosine-5-monophosphate dehydrogenase guaB1
O: Inosine-5-monophosphate dehydrogenase guaB1
P: Inosine-5-monophosphate dehydrogenase guaB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)834,33032
Polymers828,51916
Non-polymers5,81216
Water0
1
A: Inosine-5-monophosphate dehydrogenase guaB1
B: Inosine-5-monophosphate dehydrogenase guaB1
C: Inosine-5-monophosphate dehydrogenase guaB1
D: Inosine-5-monophosphate dehydrogenase guaB1
E: Inosine-5-monophosphate dehydrogenase guaB1
F: Inosine-5-monophosphate dehydrogenase guaB1
G: Inosine-5-monophosphate dehydrogenase guaB1
H: Inosine-5-monophosphate dehydrogenase guaB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,16516
Polymers414,2598
Non-polymers2,9068
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45640 Å2
ΔGint-266 kcal/mol
Surface area121270 Å2
2
I: Inosine-5-monophosphate dehydrogenase guaB1
J: Inosine-5-monophosphate dehydrogenase guaB1
K: Inosine-5-monophosphate dehydrogenase guaB1
L: Inosine-5-monophosphate dehydrogenase guaB1
M: Inosine-5-monophosphate dehydrogenase guaB1
N: Inosine-5-monophosphate dehydrogenase guaB1
O: Inosine-5-monophosphate dehydrogenase guaB1
P: Inosine-5-monophosphate dehydrogenase guaB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,16516
Polymers414,2598
Non-polymers2,9068
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45760 Å2
ΔGint-282 kcal/mol
Surface area122970 Å2
Unit cell
Length a, b, c (Å)104.788, 105.098, 170.468
Angle α, β, γ (deg.)76.916, 81.857, 69.013
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Inosine-5-monophosphate dehydrogenase guaB1


Mass: 51782.434 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_3548 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I7GA39, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium chloride 20% (v/v) PEG 3000 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→47.69 Å / Num. obs: 208443 / % possible obs: 90.06 % / Redundancy: 2.1 % / Biso Wilson estimate: 48.86 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1364 / Rpim(I) all: 0.1241 / Rrim(I) all: 0.185 / Net I/σ(I): 5.27
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.632 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 21247 / CC1/2: 0.293 / CC star: 0.673 / Rpim(I) all: 1.495 / Rrim(I) all: 2.22 / % possible all: 86.46

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Coot0.9.6model building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zfj

1zfj


Resolution: 2.5→47.6888947297 Å / SU ML: 0.552059369981 / Cross valid method: FREE R-VALUE / σ(F): 1.95835944193 / Phase error: 38.9829274508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.306029421929 10161 4.9416399183 %
Rwork0.263053609633 195459 -
obs0.265159235491 205620 90.0692537157 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.9802898605 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.6888947297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52676 0 384 0 53060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022839676240753983
X-RAY DIFFRACTIONf_angle_d1.0871740939873608
X-RAY DIFFRACTIONf_chiral_restr0.03969539074148829
X-RAY DIFFRACTIONf_plane_restr0.003500538487629633
X-RAY DIFFRACTIONf_dihedral_angle_d13.353279986618814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.4552594183633020.3790403224375635X-RAY DIFFRACTION78.5837193911
2.5284-2.55810.4304061130013340.3838621036316560X-RAY DIFFRACTION89.8592283629
2.5581-2.58930.4155812894083280.3804294208846557X-RAY DIFFRACTION90.8790918691
2.5893-2.62210.4376506653164030.3739743153016567X-RAY DIFFRACTION90.8380033885
2.6221-2.65660.4363927197943530.3794812757416481X-RAY DIFFRACTION91.266025641
2.6566-2.6930.4299028261813000.3886659726486623X-RAY DIFFRACTION89.9909008189
2.693-2.73150.4118716441923360.3737693759496543X-RAY DIFFRACTION91.6833266693
2.7315-2.77220.4274646471433450.3652873370736764X-RAY DIFFRACTION92.3007011166
2.7722-2.81560.4218419628033830.3598747297566558X-RAY DIFFRACTION91.7393602961
2.8156-2.86170.3852317106913230.3553025023356624X-RAY DIFFRACTION91.4560294892
2.8617-2.91110.3996952827183620.3431520146186646X-RAY DIFFRACTION90.812491901
2.9111-2.9640.3787575817563650.3290655903856359X-RAY DIFFRACTION89.4030049196
2.964-3.0210.4122051878413190.3280222902236285X-RAY DIFFRACTION86.6325593598
3.021-3.08260.3525325738512830.3110444355216073X-RAY DIFFRACTION82.7281010022
3.0826-3.14960.3671828523613410.319361503616774X-RAY DIFFRACTION94.2009797431
3.1496-3.22290.3634026406523300.3077550257746823X-RAY DIFFRACTION94.0936595633
3.2229-3.30350.356259014983540.2967905244876745X-RAY DIFFRACTION93.2728944948
3.3035-3.39280.3765536684083240.2940452175926829X-RAY DIFFRACTION93.2837767345
3.3928-3.49260.3425728274793310.2919248603236547X-RAY DIFFRACTION90.4167214408
3.4926-3.60530.3299166261073510.2735704018426664X-RAY DIFFRACTION92.1450151057
3.6053-3.73410.3011186131383650.265526589156326X-RAY DIFFRACTION87.9237844941
3.7341-3.88350.3008612731493390.2490935220126301X-RAY DIFFRACTION87.5065893516
3.8835-4.06020.280234213372960.2395968847845884X-RAY DIFFRACTION81.1556139199
4.0602-4.27410.2544613093363220.2157973766796769X-RAY DIFFRACTION93.721913825
4.2741-4.54170.2450194278723870.2090603573926753X-RAY DIFFRACTION93.5534591195
4.5417-4.89210.2544988284123260.2097585840386726X-RAY DIFFRACTION93.095709571
4.8921-5.38380.2446780171023500.2127823319036618X-RAY DIFFRACTION91.2639161755
5.3838-6.16140.2875389861963360.2321328477226199X-RAY DIFFRACTION85.6712113267
6.1614-7.75730.2367429821593120.2121670495496781X-RAY DIFFRACTION93.3658022904
7.7573-47.68889472970.1953132524423610.1778273512276445X-RAY DIFFRACTION89.3527635552

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