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- PDB-8c53: Trypanosoma brucei IMP dehydrogenase (ori) crystallized in High F... -

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Basic information

Entry
Database: PDB / ID: 8c53
TitleTrypanosoma brucei IMP dehydrogenase (ori) crystallized in High Five cells reveals native ligands ATP, GDP and phosphate. Diffraction data collection at 100 K in cellulo; CrystFEL processing
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsTRANSFERASE / IMP dehydrogenase / purine biosynthetic enzyme / native cofactors
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
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLahey-Rudolph, J.M. / Schoenherr, R. / Boger, J. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Duden, R. / Bourenkov, G. / Schneider, T. / Redecke, L.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research05K18FLA, InCellSX Germany
Joachim Herz StiftungPhD scholarship Germany
German Research Foundation (DFG)EXC306 Germany
CitationJournal: Nat Commun / Year: 2024
Title: A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst.
Authors: Schonherr, R. / Boger, J. / Lahey-Rudolph, J.M. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Duden, R. / Konig, P. / Bourenkov, G. / Schneider, T.R. / Redecke, L.
History
DepositionJan 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name

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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)113,6228
Polymers111,5312
Non-polymers2,0916
Water2,702150
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)454,48832
Polymers446,1258
Non-polymers8,36324
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 area44650 Å2
ΔGint-259 kcal/mol
Surface area131770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.900, 206.900, 92.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
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
Noncrystallographic symmetry (NCS)NCS oper: (Code: givenMatrix: (0.498633116137, -0.86677619989, -0.00800217442322), (-0.866793669248, -0.498662541492, 0.00209872922587), (-0.00580951317835, 0.00588973823644, -0.999965779685)Vector: ...NCS oper: (Code: given
Matrix: (0.498633116137, -0.86677619989, -0.00800217442322), (-0.866793669248, -0.498662541492, 0.00209872922587), (-0.00580951317835, 0.00588973823644, -0.999965779685)
Vector: 89.6028137276, 155.175132244, 12.2921625992)

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Components

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


Mass: 55765.656 Da / Num. of mol.: 2 / Mutation: T488S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pFB1 / Details (production host): ori / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P50098, IMP dehydrogenase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.43 Å3/Da / Density % sol: 72.22 %
Crystal growTemperature: 300 K / Method: in cell
Details: crystallized in rBV Tb IMPDH ori (MOI 1) infected High Five cells, in adhesion culture using ESF921 cell culture medium.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.299→57.38 Å / Num. obs: 89070 / % possible obs: 99.88 % / Redundancy: 3667 % / Biso Wilson estimate: 52.99 Å2 / CC1/2: 0.9976 / CC star: 0.9994 / R split: 0.0862 / Net I/σ(I): 10.06
Reflection shellResolution: 2.299→2.33 Å / Redundancy: 1246 % / Num. unique obs: 5857 / CC1/2: 0.1957 / CC star: 0.5722 / R split: 1.9952 / % possible all: 99.09
Serial crystallography sample deliveryDescription: mesh mounts / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: mesh grid / Support base: goniometer
Serial crystallography data reductionFrames indexed: 75741 / Frames total: 96949 / Lattices indexed: 82831

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158-000refinement
MxCuBEdata collection
CrystFEL1.10.0data reduction
CrystFEL1.9.0data scaling
PHASER1.19.2_4158-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JCN

1jcn


Resolution: 2.3→57.38 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 1078 1.21 %
Rwork0.2083 --
obs0.2087 88954 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→57.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6731 0 128 150 7009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067033
X-RAY DIFFRACTIONf_angle_d0.7279541
X-RAY DIFFRACTIONf_dihedral_angle_d7.996991
X-RAY DIFFRACTIONf_chiral_restr0.0441093
X-RAY DIFFRACTIONf_plane_restr0.0051210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.342313310771X-RAY DIFFRACTION99
2.4-2.530.3671330.332210839X-RAY DIFFRACTION100
2.53-2.690.33661330.285710882X-RAY DIFFRACTION100
2.69-2.90.27691330.262910902X-RAY DIFFRACTION100
2.9-3.190.31371350.235710953X-RAY DIFFRACTION100
3.19-3.650.26371340.214210963X-RAY DIFFRACTION100
3.65-4.60.18981360.166211085X-RAY DIFFRACTION100
4.6-57.380.20221410.173911481X-RAY DIFFRACTION100

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