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- PDB-9hg0: Crystal structure of M. smegmatis GMP reductase with XMP* intermi... -

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Basic information

Entry
Database: PDB / ID: 9hg0
TitleCrystal structure of M. smegmatis GMP reductase with XMP* intermidiate in complex with NADP+ and IMP.
ComponentsGMP reductase
KeywordsOXIDOREDUCTASE / GMP reductase / GuaB1 / CBS domain / Mycobacterium smegmatis
Function / homology
Function and homology information


GMP reductase / GMP reductase activity / IMP salvage / IMP dehydrogenase activity / purine ribonucleoside salvage / cytosol
Similarity search - Function
GMP reductase-like / : / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
INOSINIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GMP reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDolezal, M. / Pichova, I.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: To Be Published
Title: Structural basis for allosteric regulation of mycobacterial guanosine 5'-monophosphate reductase with ATP and GTP.
Authors: Dolezal, M. / Knejzlik, Z. / Kouba, T. / Filimonenko, A. / Svachova, H. / Klima, M. / Pichova, I.
History
DepositionNov 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GMP reductase
B: GMP reductase
C: GMP reductase
D: GMP reductase
E: GMP reductase
F: GMP reductase
G: GMP reductase
H: GMP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,77832
Polymers414,2598
Non-polymers11,51924
Water13,349741
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56710 Å2
ΔGint-255 kcal/mol
Surface area125400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.800, 204.910, 116.150
Angle α, β, γ (deg.)90.000, 102.306, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
GMP reductase / Guanosine 5'-monophosphate reductase / GMPR


Mass: 51782.434 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: guaB1, MSMEG_3634, MSMEI_3548 / Plasmid: pTriex / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QYE8, GMP reductase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.03 M Magnesium chloride 0.03 M Calcium chloride 20% (v/v) Ethylene glycol 8.5% (v/v) PEG 8000 0.1 M Tris/BICINE, pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2024
RadiationMonochromator: DCD Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→42.55 Å / Num. obs: 533989 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 45.85 Å2 / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.1688 / Rpim(I) all: 0.1052 / Rrim(I) all: 0.1995 / Net I/σ(I): 3.7
Reflection shellResolution: 2.1→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 2.21 / Mean I/σ(I) obs: 0.61 / Num. unique obs: 17667 / CC1/2: 0.171 / CC star: 0.541 / Rpim(I) all: 1.349 / Rrim(I) all: 2.596 / % possible all: 99.07

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Processing

Software
NameVersionClassification
XDS20230630data reduction
XSCALE20230630data scaling
PHASER2.8.3phasing
Coot0.9.8.1 ELmodel building
PHENIX1.21_5204refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.55 Å / SU ML: 0.3157 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2485 13469 5 %
Rwork0.2185 255932 -
obs0.22 269401 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.59 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27384 0 752 741 28877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002328656
X-RAY DIFFRACTIONf_angle_d0.524239182
X-RAY DIFFRACTIONf_chiral_restr0.04184648
X-RAY DIFFRACTIONf_plane_restr0.00545214
X-RAY DIFFRACTIONf_dihedral_angle_d14.994210442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.34074440.32948428X-RAY DIFFRACTION99.07
2.12-2.150.37014490.33228522X-RAY DIFFRACTION99.06
2.15-2.170.34674470.31928480X-RAY DIFFRACTION99.16
2.17-2.20.33754480.31518535X-RAY DIFFRACTION99.13
2.2-2.230.33144480.30018519X-RAY DIFFRACTION99.19
2.23-2.260.33724440.29258468X-RAY DIFFRACTION99.12
2.26-2.290.32674490.29678506X-RAY DIFFRACTION99.2
2.29-2.330.32264500.28588551X-RAY DIFFRACTION99.51
2.33-2.370.29854470.26258505X-RAY DIFFRACTION99.43
2.37-2.40.31074460.26078458X-RAY DIFFRACTION98.74
2.4-2.450.30674410.25868384X-RAY DIFFRACTION98.07
2.45-2.490.29074530.25038617X-RAY DIFFRACTION99.92
2.49-2.540.28164500.24288549X-RAY DIFFRACTION99.94
2.54-2.590.28964540.24318630X-RAY DIFFRACTION99.93
2.59-2.650.28894480.23198525X-RAY DIFFRACTION99.92
2.65-2.710.26744500.24658541X-RAY DIFFRACTION99.8
2.71-2.770.27614520.23388592X-RAY DIFFRACTION99.69
2.77-2.850.26524490.23288525X-RAY DIFFRACTION99.63
2.85-2.930.30794490.25868529X-RAY DIFFRACTION99.44
2.93-3.030.28354500.25088550X-RAY DIFFRACTION99.47
3.03-3.140.27624480.24458539X-RAY DIFFRACTION99
3.14-3.260.28094480.2378504X-RAY DIFFRACTION99.04
3.26-3.410.2574480.23248515X-RAY DIFFRACTION99.08
3.41-3.590.25374420.22818386X-RAY DIFFRACTION97.93
3.59-3.820.23014550.20738649X-RAY DIFFRACTION99.95
3.82-4.110.21394530.19228597X-RAY DIFFRACTION99.96
4.11-4.520.20654520.17758606X-RAY DIFFRACTION99.93
4.52-5.180.20434540.1778620X-RAY DIFFRACTION99.87
5.18-6.520.2274510.20248552X-RAY DIFFRACTION99.01
6.52-42.550.18654500.16438550X-RAY DIFFRACTION97.87

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