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- PDB-9hg3: Crystal structure of M. smegmatis GMP reductase in complex with G... -

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Basic information

Entry
Database: PDB / ID: 9hg3
TitleCrystal structure of M. smegmatis GMP reductase in complex with GMP and GTP.
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
GUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / GMP reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)421,35124
Polymers414,2598
Non-polymers7,09116
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43770 Å2
ΔGint-235 kcal/mol
Surface area130290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.080, 145.930, 146.320
Angle α, β, γ (deg.)90.000, 95.929, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,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-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.7
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 8.7

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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: Mar 15, 2024
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→112.5 Å / Num. obs: 410206 / % possible obs: 98.42 % / Redundancy: 3.5 % / Biso Wilson estimate: 57.68 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1591 / Rpim(I) all: 0.09933 / Rrim(I) all: 0.1881 / Net I/σ(I): 5.03
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 3.5 % / Rmerge(I) obs: 4.465 / Mean I/σ(I) obs: 0.22 / Num. unique obs: 13569 / CC1/2: 0.087 / CC star: 0.4 / Rpim(I) all: 2.785 / Rrim(I) all: 5.277 / % possible all: 87.28

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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: 2.3→112.48 Å / SU ML: 0.489 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.6976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2739 10300 5 %
Rwork0.2496 195541 -
obs0.2508 205841 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→112.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26752 0 448 0 27200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227928
X-RAY DIFFRACTIONf_angle_d0.433638184
X-RAY DIFFRACTIONf_chiral_restr0.04124528
X-RAY DIFFRACTIONf_plane_restr0.00415048
X-RAY DIFFRACTIONf_dihedral_angle_d10.394810168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.41342980.41845719X-RAY DIFFRACTION87.28
2.33-2.350.41113310.40346164X-RAY DIFFRACTION92.52
2.35-2.380.44133350.39736300X-RAY DIFFRACTION96.15
2.38-2.410.43633340.38766333X-RAY DIFFRACTION96.61
2.41-2.440.39383430.38696493X-RAY DIFFRACTION97.88
2.44-2.480.39173390.37526454X-RAY DIFFRACTION97.54
2.48-2.510.37583400.35966474X-RAY DIFFRACTION97.69
2.51-2.550.39763460.35796555X-RAY DIFFRACTION99.75
2.55-2.590.36753470.34256585X-RAY DIFFRACTION99.81
2.59-2.630.36473470.32956621X-RAY DIFFRACTION99.74
2.63-2.680.32433460.32646574X-RAY DIFFRACTION99.75
2.68-2.730.35683470.31796573X-RAY DIFFRACTION99.77
2.73-2.780.36543460.32226589X-RAY DIFFRACTION99.74
2.78-2.840.34223480.32446600X-RAY DIFFRACTION99.54
2.84-2.90.34133470.32676591X-RAY DIFFRACTION99.57
2.9-2.970.36643460.33056581X-RAY DIFFRACTION99.55
2.97-3.040.34613470.3146577X-RAY DIFFRACTION99.47
3.04-3.120.32213470.29726589X-RAY DIFFRACTION99.57
3.12-3.210.31093450.28386560X-RAY DIFFRACTION99.38
3.21-3.320.32523450.2676556X-RAY DIFFRACTION98.94
3.32-3.440.30053480.26516612X-RAY DIFFRACTION99.91
3.44-3.570.30613490.26196623X-RAY DIFFRACTION99.86
3.57-3.740.29313480.24156636X-RAY DIFFRACTION99.83
3.74-3.930.23923480.22536610X-RAY DIFFRACTION99.78
3.93-4.180.20983470.2036595X-RAY DIFFRACTION99.27
4.18-4.50.21693460.19176558X-RAY DIFFRACTION98.91
4.5-4.950.2293440.19876525X-RAY DIFFRACTION98.13
4.96-5.670.22543500.216652X-RAY DIFFRACTION99.87
5.67-7.150.24783520.21766674X-RAY DIFFRACTION99.83
7.15-112.480.17413440.17966568X-RAY DIFFRACTION96.78

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