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- PDB-9hg1: Crystal structure of M. smegmatis GMP reductase in complex with G... -

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Basic information

Entry
Database: PDB / ID: 9hg1
TitleCrystal structure of M. smegmatis GMP reductase in complex with GMP and ATP.
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 / ADENOSINE-5'-TRIPHOSPHATE / GMP reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDolezal, M. / Klima, 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
I: GMP reductase
J: GMP reductase
K: GMP reductase
L: GMP reductase
M: GMP reductase
N: GMP reductase
O: GMP reductase
P: GMP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)842,44548
Polymers828,51916
Non-polymers13,92632
Water16,826934
1
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)421,22324
Polymers414,2598
Non-polymers6,96316
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53350 Å2
ΔGint-276 kcal/mol
Surface area125480 Å2
MethodPISA
2
I: GMP reductase
J: GMP reductase
K: GMP reductase
L: GMP reductase
M: GMP reductase
N: GMP reductase
O: GMP reductase
P: GMP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,22324
Polymers414,2598
Non-polymers6,96316
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53440 Å2
ΔGint-270 kcal/mol
Surface area125840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.570, 113.600, 178.060
Angle α, β, γ (deg.)82.700, 77.236, 66.749
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
GMP reductase / Guanosine 5'-monophosphate reductase / GMPR


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: guaB1, MSMEG_3634, MSMEI_3548 / Plasmid: pTriex / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QYE8, GMP reductase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 934 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium chloride 23% (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: 14.3 / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2019
RadiationMonochromator: CCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.296→49.33 Å / Num. obs: 670661 / % possible obs: 96.31 % / Redundancy: 3.3 % / Biso Wilson estimate: 44.88 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08289 / Rpim(I) all: 0.05265 / Rrim(I) all: 0.09856 / Net I/σ(I): 8.17
Reflection shellResolution: 2.3→2.32 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.8155 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 14135 / CC1/2: 0.428 / CC star: 0.774 / Rpim(I) all: 0.6748 / Rrim(I) all: 1.066 / % possible all: 63.42

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Processing

Software
NameVersionClassification
XDS20220220data reduction
XSCALE20220220data scaling
PHASER2.8.2phasing
Coot0.9.8.1 ELmodel building
PHENIX1.21_5204refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.33 Å / SU ML: 0.2987 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.2029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 16984 5 %
Rwork0.1997 322625 -
obs0.2012 339609 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54724 0 880 934 56538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003657220
X-RAY DIFFRACTIONf_angle_d0.582478284
X-RAY DIFFRACTIONf_chiral_restr0.04449248
X-RAY DIFFRACTIONf_plane_restr0.005810376
X-RAY DIFFRACTIONf_dihedral_angle_d12.38920748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.320.29933710.29537048X-RAY DIFFRACTION63.42
2.32-2.350.32474590.28038730X-RAY DIFFRACTION77.61
2.35-2.380.31244850.27759211X-RAY DIFFRACTION82.74
2.38-2.410.32165210.2689887X-RAY DIFFRACTION88.88
2.41-2.440.33385560.26910573X-RAY DIFFRACTION94.59
2.44-2.470.30095790.258710994X-RAY DIFFRACTION98.35
2.47-2.510.31325850.252211128X-RAY DIFFRACTION98.92
2.51-2.550.28615800.241811016X-RAY DIFFRACTION98.98
2.55-2.590.28425810.241111038X-RAY DIFFRACTION99.1
2.59-2.630.28725830.242811065X-RAY DIFFRACTION99.13
2.63-2.670.27895800.251411030X-RAY DIFFRACTION99.11
2.67-2.720.30225840.250611085X-RAY DIFFRACTION99.04
2.72-2.770.29595800.246911019X-RAY DIFFRACTION98.43
2.77-2.830.28735850.251111115X-RAY DIFFRACTION99.55
2.83-2.890.29285860.25211142X-RAY DIFFRACTION99.48
2.89-2.960.31525860.256511136X-RAY DIFFRACTION99.58
2.96-3.030.29285830.251411076X-RAY DIFFRACTION99.61
3.03-3.120.27015870.23711138X-RAY DIFFRACTION99.7
3.12-3.210.28085830.232111083X-RAY DIFFRACTION99.28
3.21-3.310.26845840.229911097X-RAY DIFFRACTION98.98
3.31-3.430.26955860.226311139X-RAY DIFFRACTION99.79
3.43-3.570.24815850.211711100X-RAY DIFFRACTION99.65
3.57-3.730.22375840.197911094X-RAY DIFFRACTION99.72
3.73-3.930.20255870.18111158X-RAY DIFFRACTION99.59
3.93-4.170.18935810.169211030X-RAY DIFFRACTION98.66
4.17-4.490.1785840.157111114X-RAY DIFFRACTION99.89
4.49-4.950.16745890.150111189X-RAY DIFFRACTION99.8
4.95-5.660.18945870.164911134X-RAY DIFFRACTION99.64
5.66-7.130.19445780.172710996X-RAY DIFFRACTION98.82
7.13-49.330.15285850.139611060X-RAY DIFFRACTION99.05

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