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- PDB-6rfu: In cellulo crystallization of Trypanosoma brucei IMP dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 6rfu
TitleIn cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of ATP and GMP as genuine co-factors
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsIMMUNOSUPPRESSANT / IMP dehydrogenase / Trypanosoma brucei / in cellulo crystallization / FEL
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / glycosome / GMP biosynthetic process / nucleotide binding / metal ion binding
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 / 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'-MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNass, K. / Redecke, L. / Perbandt, M. / Yefanov, O. / Gabdulkhakov, A. / Duszenko, M. / Chapman, H.N. / Betzel, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationEXC 1074 - project ID 194651731. Germany
German Federal Ministry for Education and Research05K2018-2017-06734 Germany
CitationJournal: Nat Commun / Year: 2020
Title: In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors.
Authors: Nass, K. / Redecke, L. / Perbandt, M. / Yefanov, O. / Klinge, M. / Koopmann, R. / Stellato, F. / Gabdulkhakov, A. / Schonherr, R. / Rehders, D. / Lahey-Rudolph, J.M. / Aquila, A. / Barty, A. ...Authors: Nass, K. / Redecke, L. / Perbandt, M. / Yefanov, O. / Klinge, M. / Koopmann, R. / Stellato, F. / Gabdulkhakov, A. / Schonherr, R. / Rehders, D. / Lahey-Rudolph, J.M. / Aquila, A. / Barty, A. / Basu, S. / Doak, R.B. / Duden, R. / Frank, M. / Fromme, R. / Kassemeyer, S. / Katona, G. / Kirian, R. / Liu, H. / Majoul, I. / Martin-Garcia, J.M. / Messerschmidt, M. / Shoeman, R.L. / Weierstall, U. / Westenhoff, S. / White, T.A. / Williams, G.J. / Yoon, C.H. / Zatsepin, N. / Fromme, P. / Duszenko, M. / Chapman, H.N. / Betzel, C.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3006
Polymers111,5592
Non-polymers1,7414
Water39622
1
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)453,20124
Polymers446,2378
Non-polymers6,96316
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area40300 Å2
ΔGint-126 kcal/mol
Surface area136030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.000, 209.000, 92.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Inosine-5'-monophosphate dehydrogenase / IMPDH


Mass: 55779.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote)
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P50098, IMP dehydrogenase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 4.5 Å3/Da / Density % sol: 72.68 %
Crystal growTemperature: 291 K / Method: in cell / Details: In cellulo upon cell growth

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 2.07 Å
DetectorType: CS-PAD XPP / Detector: PIXEL / Date: Jan 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07 Å / Relative weight: 1
ReflectionResolution: 2.8→52.3 Å / Num. obs: 50656 / % possible obs: 100 % / Redundancy: 187 % / Net I/σ(I): 4.14
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 3557

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Processing

Software
NameClassification
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JCN

1jcn


Resolution: 2.8→52.3 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs50656 100 %
Refinement stepCycle: LAST / Resolution: 2.8→52.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6777 0 110 22 6909

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