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- PDB-9hfz: Crystal structure of M. smegmatis GMP reductase in complex with IMP. -

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Basic information

Entry
Database: PDB / ID: 9hfz
TitleCrystal structure of M. smegmatis GMP reductase in complex with 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 / GMP reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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)419,83124
Polymers414,2598
Non-polymers5,57116
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42770 Å2
ΔGint-252 kcal/mol
Surface area129700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.910, 145.910, 146.210
Angle α, β, γ (deg.)90.000, 95.628, 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-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
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: 60.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.03 M Magnesium chloride 0.03 M Calcium chloride 20% (v/v) Ethylene glycol 10.0% (v/v) PEG 8000 0.1 M Tris/BICINE, pH 8.5

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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 6M / Detector: PIXEL / Date: Jul 10, 2020
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: 2.8→48.11 Å / Num. obs: 222592 / % possible obs: 97.93 % / Redundancy: 2 % / Biso Wilson estimate: 69.78 Å2 / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.1935 / Rpim(I) all: 0.1759 / Rrim(I) all: 0.2622 / Net I/σ(I): 2.83
Reflection shellResolution: 2.8→2.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 1.922 / Mean I/σ(I) obs: 0.38 / Num. unique obs: 7232 / CC1/2: 0.143 / CC star: 0.5 / Rpim(I) all: 1.747 / Rrim(I) all: 2.605 / % possible all: 93.02

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Processing

Software
NameVersionClassification
XDS20200417data reduction
XSCALE20220220data scaling
PHASER2.8.3phasing
Coot0.9.8.1 ELmodel building
PHENIX1.21_5204refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.11 Å / SU ML: 0.5891 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.1421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3523 5684 5 %
Rwork0.324 107891 -
obs0.3254 113575 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26650 0 368 0 27018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227474
X-RAY DIFFRACTIONf_angle_d0.46437474
X-RAY DIFFRACTIONf_chiral_restr0.04094494
X-RAY DIFFRACTIONf_plane_restr0.00384946
X-RAY DIFFRACTIONf_dihedral_angle_d11.54099882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.4421790.40483418X-RAY DIFFRACTION93.02
2.83-2.870.39581770.40373334X-RAY DIFFRACTION91.27
2.87-2.90.43671900.40563535X-RAY DIFFRACTION97.31
2.9-2.940.38381900.39313606X-RAY DIFFRACTION99.09
2.94-2.980.42661920.38133669X-RAY DIFFRACTION99.03
2.98-3.020.4411890.3873593X-RAY DIFFRACTION99.4
3.02-3.060.40341920.37263650X-RAY DIFFRACTION98.97
3.06-3.10.36021900.36813610X-RAY DIFFRACTION99.16
3.1-3.150.37451900.37153611X-RAY DIFFRACTION99.04
3.15-3.210.43451920.38443634X-RAY DIFFRACTION98.94
3.21-3.260.43611910.38193641X-RAY DIFFRACTION99.12
3.26-3.320.36181920.35333644X-RAY DIFFRACTION98.66
3.32-3.380.39331890.3533585X-RAY DIFFRACTION98.98
3.38-3.450.34781900.34843599X-RAY DIFFRACTION98.52
3.45-3.530.37141830.33643486X-RAY DIFFRACTION95.08
3.53-3.610.36091910.32973636X-RAY DIFFRACTION99.07
3.61-3.70.35491910.32393632X-RAY DIFFRACTION99.38
3.7-3.80.38181900.31973626X-RAY DIFFRACTION98.89
3.8-3.910.37231930.31693652X-RAY DIFFRACTION98.79
3.91-4.040.35951910.31623627X-RAY DIFFRACTION98.68
4.04-4.180.3371920.29723658X-RAY DIFFRACTION99.07
4.18-4.350.28911900.27823595X-RAY DIFFRACTION98.93
4.35-4.550.31541910.30083619X-RAY DIFFRACTION98.35
4.55-4.790.32861840.30073520X-RAY DIFFRACTION96.13
4.79-5.090.32881930.29873658X-RAY DIFFRACTION98.92
5.09-5.480.29991920.30053654X-RAY DIFFRACTION99.3
5.48-6.030.34571930.31273652X-RAY DIFFRACTION99
6.03-6.90.37451880.32443560X-RAY DIFFRACTION95.91
6.9-8.680.33681920.31073649X-RAY DIFFRACTION98.13
8.68-48.110.31841870.29673538X-RAY DIFFRACTION93.81

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