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- PDB-7s87: Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium... -

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Basic information

Entry
Database: PDB / ID: 7s87
TitleCrystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor / DHODH / TIM Barrel / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Pyrimidine biosynthesis / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-8IE / ACETATE ION / FLAVIN MONONUCLEOTIDE / OROTIC ACID / polyethylene glycol / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Shek, R. / Abendroth, J. / Lorimer, D. / Edwards, T.E. / Eastman, R. / Van Voorhis, W.
History
DepositionSep 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
B: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,25214
Polymers90,7722
Non-polymers3,48112
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-48 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.726, 161.093, 92.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-604-

ACT

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 155 through 192 or (resid 193...A155 - 205
121(chain 'A' and (resid 155 through 192 or (resid 193...A208 - 373
131(chain 'A' and (resid 155 through 192 or (resid 193...A384 - 535
141(chain 'A' and (resid 155 through 192 or (resid 193...A556
151(chain 'A' and (resid 155 through 192 or (resid 193...A571
161(chain 'A' and (resid 155 through 192 or (resid 193...A573
171(chain 'A' and (resid 155 through 192 or (resid 193...A593
281(chain 'B' and ((resid 155 through 156 and (name N...B155 - 205
291(chain 'B' and ((resid 155 through 156 and (name N...B208 - 373
2101(chain 'B' and ((resid 155 through 156 and (name N...B384 - 535
2111(chain 'B' and ((resid 155 through 156 and (name N...B556
2121(chain 'B' and ((resid 155 through 156 and (name N...B571
2131(chain 'B' and ((resid 155 through 156 and (name N...B573
2141(chain 'B' and ((resid 155 through 156 and (name N...B593

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydroorotate dehydrogenase (quinone), mitochondrial / DHOdehase / Dihydroorotate oxidase


Mass: 45385.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFF0160c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q08210, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 7 types, 91 molecules

#2: Chemical
ChemComp-8IE / (4R)-3-methyl-5-[(4R)-4-methyl-3,4-dihydroisoquinolin-2(1H)-yl]thieno[2,3-e][1,2,4]triazolo[4,3-c]pyrimidine


Mass: 335.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17N5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H62O15
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.16 M Ammonium Sulfate, 0.1 M Sodium Acetate, 18% PEG4000, 10 mM DTT. Protein was co-crystallized with 2 mM DHOD, 5 mM NCGC00600348-01. cryo: 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→98.6 Å / Num. obs: 24145 / % possible obs: 98.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 47.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.054 / Rrim(I) all: 0.143 / Net I/σ(I): 12.2
Reflection shellResolution: 2.75→2.88 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3084 / CC1/2: 0.847 / Rrim(I) all: 0.71

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VTY

6vty


Resolution: 2.75→67.5 Å / SU ML: 0.3197 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8738 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23 1251 5.18 %
Rwork0.1698 22885 -
obs0.1728 24136 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.82 Å2
Refinement stepCycle: LAST / Resolution: 2.75→67.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5672 0 204 79 5955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556000
X-RAY DIFFRACTIONf_angle_d0.95268154
X-RAY DIFFRACTIONf_chiral_restr0.0526916
X-RAY DIFFRACTIONf_plane_restr0.00561029
X-RAY DIFFRACTIONf_dihedral_angle_d5.25394063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.36281450.26742487X-RAY DIFFRACTION98.32
2.86-2.990.27861510.21292430X-RAY DIFFRACTION94.3
2.99-3.150.2871460.19422474X-RAY DIFFRACTION98.76
3.15-3.350.25991320.18582544X-RAY DIFFRACTION98.78
3.35-3.60.21531250.15962577X-RAY DIFFRACTION98.9
3.6-3.970.21431510.15112527X-RAY DIFFRACTION98.89
3.97-4.540.19411220.14422552X-RAY DIFFRACTION97.27
4.54-5.720.21221440.14892609X-RAY DIFFRACTION99.03
5.72-67.50.20911350.17862685X-RAY DIFFRACTION97.92
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)
12.283735743830.670984048025-0.1170627544892.77575446866-0.2235583149281.059627103750.0223625243757-0.01866246093670.00880866170990.208150753277-0.121196888210.255045650725-0.0103521760742-0.1666282099610.09487743793680.231731682491-0.01641483280310.004677796126440.250907099324-0.02920945747110.2270222552338.46146.87724.208
21.80706792480.9428125380780.1311689348053.71874023183-0.6595171927011.924771438020.0897551272696-0.1330926750240.07783879321680.460559458831-0.336075976266-0.727862217571-0.4619082811270.3620302566090.1486398840180.450205800471-0.111189962573-0.1453783569150.320940346160.06817223393810.68227162053934.47588.52922.83
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 157:536 OR RESID 601:606 ) ) OR ( CHAIN B AND RESID 601:601 )A157 - 536
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 157:536 OR RESID 601:606 ) ) OR ( CHAIN B AND RESID 601:601 )A601 - 606
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 157:536 OR RESID 601:606 ) ) OR ( CHAIN B AND RESID 601:601 )B601
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 155:536 OR RESID 602:605 ) ) OR ( CHAIN A AND RESID 607:607 )B155 - 536
5X-RAY DIFFRACTION2( CHAIN B AND ( RESID 155:536 OR RESID 602:605 ) ) OR ( CHAIN A AND RESID 607:607 )B602 - 605
6X-RAY DIFFRACTION2( CHAIN B AND ( RESID 155:536 OR RESID 602:605 ) ) OR ( CHAIN A AND RESID 607:607 )A607

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