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- PDB-6lk4: Crystal structure of GMP reductase from Trypanosoma brucei in com... -

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Basic information

Entry
Database: PDB / ID: 6lk4
TitleCrystal structure of GMP reductase from Trypanosoma brucei in complex with guanosine 5'-triphosphate
ComponentsGuanosine 5'-monophosphate Reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / 5'-monophosphate reductase / guanosine 5'-triphosphate / cystathionine beta synthase motif
Function / homology
Function and homology information


GMP reductase activity / IMP dehydrogenase activity / IMP dehydrogenase / glycosome / GMP biosynthetic process / GTP biosynthetic process / nucleolus / metal ion binding / cytoplasm
Similarity search - Function
IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsMase, H. / Otani, T. / Imamura, A. / Nishimura, S. / Inui, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)25660231 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)25242046 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K19329 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Allosteric regulation accompanied by oligomeric state changes of Trypanosoma brucei GMP reductase through cystathionine-beta-synthase domain.
Authors: Imamura, A. / Okada, T. / Mase, H. / Otani, T. / Kobayashi, T. / Tamura, M. / Kubata, B.K. / Inoue, K. / Rambo, R.P. / Uchiyama, S. / Ishii, K. / Nishimura, S. / Inui, T.
History
DepositionDec 18, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 18, 2020ID: 5X8O
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanosine 5'-monophosphate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4563
Polymers53,8381
Non-polymers6182
Water543
1
A: Guanosine 5'-monophosphate Reductase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)435,65124
Polymers430,7068
Non-polymers4,94516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area33380 Å2
ΔGint-238 kcal/mol
Surface area119840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.107, 144.107, 135.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 53838.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57ZS7, GMP reductase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Source detailsThe source organism of sequence reference UniProtKB entry Q57ZS7 (Q57ZS7_TRYB2), is described as ...The source organism of sequence reference UniProtKB entry Q57ZS7 (Q57ZS7_TRYB2), is described as 'Trypanosoma brucei brucei (strain 927/4 GUTat10.1)'. But, in this study, the gene for TbGMPR was isolated from Trypanosoma brucei brucei (strain ILTat1.4). The amino acid sequences of the enzymes from two strains are identical.

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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: 3.25 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 0.8M NaH2PO4, 0.8M KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.4 Å / Num. obs: 24874 / % possible obs: 99.9 % / Redundancy: 24.4 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Net I/σ(I): 43.4
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.921 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3926 / CC1/2: 0.906 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Coot0.8.6.1model building
XDS2017-10-10data scaling
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dqw

4dqw


Resolution: 2.503→33.92 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / Phase error: 26.54
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1243 5 %Random selection
Rwork0.206 ---
obs0.2077 24852 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.503→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 33 3 3016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073044
X-RAY DIFFRACTIONf_angle_d0.9384140
X-RAY DIFFRACTIONf_dihedral_angle_d7.2461837
X-RAY DIFFRACTIONf_chiral_restr0.051513
X-RAY DIFFRACTIONf_plane_restr0.005532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5034-2.60360.39381340.31312552X-RAY DIFFRACTION99
2.6036-2.72210.2981370.26062592X-RAY DIFFRACTION100
2.7221-2.86550.27431350.24722579X-RAY DIFFRACTION100
2.8655-3.04490.3041370.24652598X-RAY DIFFRACTION100
3.0449-3.27990.25751370.23492596X-RAY DIFFRACTION100
3.2799-3.60960.27781380.21652628X-RAY DIFFRACTION100
3.6096-4.13110.23791380.19172629X-RAY DIFFRACTION100
4.1311-5.20180.19151400.1732659X-RAY DIFFRACTION100
5.2018-33.920.24261470.19612776X-RAY DIFFRACTION100

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