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

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Basic information

Entry
Database: PDB / ID: 8cgy
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; XDS processing
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsTRANSFERASE / IMP dehydrogenase / purine biosynthetic enzyme / native cofactors
Function / homology
Function and homology information


glycosome / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / 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: 3 Å
AuthorsBoger, J. / Schoenherr, R. / Lahey-Rudolph, J.M. / 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
DepositionFeb 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 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
Water362
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


  • defined by author&software
  • Evidence: PISA suggests a multimeric state of eight or a 4-mer, with two copies in the asymmetric unit. Isolation of the crystals for further experiments would result in potential washing out of ...Evidence: PISA suggests a multimeric state of eight or a 4-mer, with two copies in the asymmetric unit. Isolation of the crystals for further experiments would result in potential washing out of ligands or hydrolysis, as with in cellulo crystallized but isolated IMPDH N-His of (pdb 6RFU)
  • 454 kDa, 8 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)454,48832
Polymers446,1258
Non-polymers8,36324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area44090 Å2
ΔGint-245 kcal/mol
Surface area131430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.100, 207.100, 92.500
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 / IMP dehydrogenase / IMPD / IMPDH


Mass: 55765.656 Da / Num. of mol.: 2 / Mutation: S488T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P50098, IMP dehydrogenase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-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
#3: Chemical ChemComp-GDP / GUANOSINE-5'-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
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.46 Å3/Da / Density % sol: 72.44 %
Crystal growTemperature: 300 K / Method: in cell
Details: crystallized in Trichoplusia ni (High Five) cells infected with recombinant baculovirus encoding TbIMPDH ori in adhesion culture (MOI 1)

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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: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→92.62 Å / Num. obs: 40798 / % possible obs: 99.8 % / Redundancy: 474 % / Biso Wilson estimate: 53.74 Å2 / CC1/2: 0.981 / Net I/σ(I): 20.37
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 9383 / CC1/2: 0.87
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Micro mesh mount

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→92.62 Å / SU ML: 0.3636 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.5046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 1598 3.92 %
Rwork0.1922 39189 -
obs0.194 40787 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.5 Å2
Refinement stepCycle: LAST / Resolution: 3→92.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6655 0 128 2 6785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046945
X-RAY DIFFRACTIONf_angle_d0.77459445
X-RAY DIFFRACTIONf_chiral_restr0.04471099
X-RAY DIFFRACTIONf_plane_restr0.00531197
X-RAY DIFFRACTIONf_dihedral_angle_d12.43362470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.38061430.29463484X-RAY DIFFRACTION99.15
3.1-3.210.29381420.25913494X-RAY DIFFRACTION99.92
3.21-3.340.30551430.2343509X-RAY DIFFRACTION99.95
3.34-3.490.29221440.21493523X-RAY DIFFRACTION100
3.49-3.670.25911420.20813502X-RAY DIFFRACTION100
3.67-3.90.25831450.1893551X-RAY DIFFRACTION100
3.9-4.20.21671460.17463557X-RAY DIFFRACTION100
4.2-4.630.19851450.15393567X-RAY DIFFRACTION100
4.63-5.30.18481460.15533565X-RAY DIFFRACTION100
5.3-6.670.22981480.18683643X-RAY DIFFRACTION100
6.67-92.620.19881540.18733794X-RAY DIFFRACTION99.65
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.80854240796-0.467834820923-0.5889502013480.467199458650.1907920143050.882747295697-0.0624083265701-0.132877853791-0.01929673387690.2415240252714.15711256504E-50.0658643295132-0.111915015175-0.2152148203970.01407979011990.3764004671740.0415779795587-0.009821095911830.3851493603-0.1088071847410.295211306929-19.973909751-76.93219646416.4253133926
21.948538019870.301670360481-0.08489031598281.80465477331-0.6640958152734.51732732284-0.0393760417204-0.003124618927480.01605866363510.141336126263-0.1386135504390.1745883632330.125161201717-0.7401324677830.1825137188010.4539254027540.2339004395280.02158127464110.573569100483-0.08466419337720.415962838437-43.8648246969-55.996245967739.7111840378
30.304394044377-0.894988710916-0.2403689766073.247742377651.887371167981.67219288019-0.0224915363385-0.07374286846380.03435387661290.0789166584224-0.0723432207950.109489389589-0.145374721351-0.2441818634430.09764072454760.3628102445060.1065988706730.01034491400250.496028640671-0.07658055475680.33099308551-35.1845214047-73.543019017117.1227538451
49.23701479154-1.515881124041.391737467026.857361539850.3753866828310.425245090933-0.116712148665-0.344031171619-0.008194103340230.600855399587-0.322479932094-0.411275614627-0.04033793219950.1368298533230.3411119570130.254712500340.0202425931053-0.05599791389020.272883317368-0.0745886400290.215845601746-18.7903343495-92.55251528568.06087296892
52.335286900480.05723031497-1.233492989251.626134156250.2279001646071.82613267190.095705981442-0.33630238639-0.1116843614550.355790897953-0.1730702212040.0145854418578-0.04874254227560.2491205319730.07622914550880.336471031294-0.01309169897-0.08025366181240.327974758737-0.02495150213670.297383589323-12.3098460175-81.135000063819.4730972835
64.149150873230.2512559830510.7042866484282.30825148144-1.561640247143.59077889209-0.463218194287-0.4932492420550.161675850880.08163037375050.184032635418-0.0691483264321-0.246288718089-0.1064890695160.2042064069540.295451974381-0.0318139059502-0.06872678886220.226817509425-0.09967075669230.288510442069-17.6896534556-91.079693602774.7253908856
71.646047469810.0747457234602-0.00483775724912.009871807780.05232105285070.795767153887-0.1480312798820.1788688462560.222625459948-0.2728283504410.04983914243060.087729194213-0.316948755343-0.2260180985180.05311014751010.4412485950540.114215145022-0.09094617890870.3670435998290.007628952141340.319152039522-10.1734443994-62.898144280357.1348370014
85.28267859377-0.7223908765230.3919951066265.861475383362.381891399842.08919375733-0.2578258681610.3561365368490.4440209441770.110037877749-0.211758307215-0.349178571674-0.1745476175510.08453618028110.422966843120.6882830245360.115432950235-0.02139269474660.4734084452270.04227884601470.456723666989-13.8094495406-43.002046529340.6129159219
93.152462523260.187903050744-1.015337323252.014008803121.708219838814.73313144238-0.1756147790150.008327659764820.312928614422-0.130996613364-0.3632493069770.109862922073-0.959397147466-0.3279429308430.5084057362830.5352717180490.220951131743-0.1351740574960.490520994783-0.01698673259820.506976287181-24.9878802245-41.29119344.1750251039
101.46331306726-1.292769506891.343585596812.28565743806-1.318813328521.30691236582-0.1243211474640.06162046006590.2148370468850.212666161087-0.0551061665851-0.107048302375-0.420788099547-0.09014384594330.2023794800330.4179840602780.0487682343158-0.01334347019760.310564999221-0.02534205799070.305327414409-4.98190194278-62.566960220364.756760548
110.9791609836240.06050063969010.2058044145892.74601022656-1.489918925791.600784895120.0217015977750.242246181260.00571016728509-0.4308661427440.03219474694710.02803864932920.18493207517-0.00164292559665-0.02275119385360.3188837898570.0497408554563-0.06494242359820.309091211755-0.05126851764870.296396931148-12.903126008-81.468060762559.3921580162
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 116 )AA2 - 1161 - 115
22chain 'A' and (resid 117 through 187 )AA117 - 187116 - 186
33chain 'A' and (resid 188 through 317 )AA188 - 317187 - 316
44chain 'A' and (resid 318 through 351 )AA318 - 351317 - 342
55chain 'A' and (resid 352 through 493 )AA352 - 493343 - 446
66chain 'B' and (resid 2 through 41 )BD2 - 411 - 40
77chain 'B' and (resid 42 through 115 )BD42 - 11541 - 114
88chain 'B' and (resid 116 through 147 )BD116 - 147115 - 146
99chain 'B' and (resid 148 through 197 )BD148 - 197147 - 196
1010chain 'B' and (resid 198 through 351 )BD198 - 351197 - 340
1111chain 'B' and (resid 352 through 493 )BD352 - 493341 - 447

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