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- PDB-6jl8: Crystal structure of GMP reductase C318A from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 6jl8
TitleCrystal structure of GMP reductase C318A from Trypanosoma brucei
ComponentsGMP reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / 5'-monophosphate reductase / 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
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsMase, H. / 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
DepositionMar 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 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: GMP reductase
B: GMP reductase


Theoretical massNumber of molelcules
Total (without water)107,6122
Polymers107,6122
Non-polymers00
Water34219
1
A: GMP reductase
B: GMP reductase

A: GMP reductase
B: GMP reductase

A: GMP reductase
B: GMP reductase

A: GMP reductase
B: GMP reductase


Theoretical massNumber of molelcules
Total (without water)430,4498
Polymers430,4498
Non-polymers00
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
Buried area28540 Å2
ΔGint-201 kcal/mol
Surface area134810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.564, 124.564, 540.174
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 GMP reductase / / Guanosine-5'-monophosphate reductase


Mass: 53806.180 Da / Num. of mol.: 2 / Mutation: C318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain ILTat1.4) (eukaryote)
Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57ZS7, GMP reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Sequence 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: 4.87 Å3/Da / Density % sol: 74.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M imidazole/hydrochloric acid (pH 8.0), 3% (w/v) PEG 3350, 0.35M lithium sulfate

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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: Jan 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.51 Å / Num. obs: 52835 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Net I/σ(I): 18.2
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.91 / Num. unique obs: 8338 / CC1/2: 0.927 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Coot0.8.6.1model building
XDS2018-01-26data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IHY

6ihy
PDB Unreleased entry


Resolution: 2.804→21.807 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.54
RfactorNum. reflection% reflection
Rfree0.258 2635 5 %
Rwork0.2232 --
obs0.2249 52689 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.804→21.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6115 0 0 19 6134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096169
X-RAY DIFFRACTIONf_angle_d1.0178388
X-RAY DIFFRACTIONf_dihedral_angle_d3.4083744
X-RAY DIFFRACTIONf_chiral_restr0.0551058
X-RAY DIFFRACTIONf_plane_restr0.0071100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8037-2.85460.39971350.32562564X-RAY DIFFRACTION98
2.8546-2.90930.31411360.28992574X-RAY DIFFRACTION100
2.9093-2.96860.30181370.27832606X-RAY DIFFRACTION100
2.9686-3.0330.30341360.26942592X-RAY DIFFRACTION100
3.033-3.10330.31741360.26722584X-RAY DIFFRACTION100
3.1033-3.18070.30561370.2662601X-RAY DIFFRACTION100
3.1807-3.26640.33611370.25682599X-RAY DIFFRACTION100
3.2664-3.36220.27661380.24592619X-RAY DIFFRACTION100
3.3622-3.47030.24891370.24382606X-RAY DIFFRACTION100
3.4703-3.59380.29751380.22522621X-RAY DIFFRACTION100
3.5938-3.7370.23331370.20892600X-RAY DIFFRACTION100
3.737-3.90620.26141380.21252629X-RAY DIFFRACTION100
3.9062-4.11080.24141380.18922621X-RAY DIFFRACTION100
4.1108-4.36650.21591390.18012633X-RAY DIFFRACTION100
4.3665-4.70050.18311390.17542654X-RAY DIFFRACTION100
4.7005-5.16780.24041410.1922679X-RAY DIFFRACTION100
5.1678-5.90260.26181420.24322690X-RAY DIFFRACTION100
5.9026-7.38830.25571430.24292721X-RAY DIFFRACTION100
7.3883-21.80720.25711510.21612861X-RAY DIFFRACTION100

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