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- PDB-7ut5: Acinetobacter baumannii dihydroorotate dehydrogenase bound with i... -

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Basic information

Entry
Database: PDB / ID: 7ut5
TitleAcinetobacter baumannii dihydroorotate dehydrogenase bound with inhibitor DSM186
ComponentsDihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE/INHIBITOR / inhibitor / complex / Flavoprotein / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-OBR / OROTIC ACID / Dihydroorotate dehydrogenase (quinone)
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDeng, X. / Phillips, M. / Tomchick, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103947 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56AI129986 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Repurposed dihydroorotate dehydrogenase inhibitors with efficacy against drug-resistant Acinetobacter baumannii.
Authors: Russo, T.A. / Umland, T.C. / Deng, X. / El Mazouni, F. / Kokkonda, S. / Olson, R. / Carlino-MacDonald, U. / Beanan, J. / Alvarado, C.L. / Tomchick, D.R. / Hutson, A. / Chen, H. / Posner, B. ...Authors: Russo, T.A. / Umland, T.C. / Deng, X. / El Mazouni, F. / Kokkonda, S. / Olson, R. / Carlino-MacDonald, U. / Beanan, J. / Alvarado, C.L. / Tomchick, D.R. / Hutson, A. / Chen, H. / Posner, B. / Rathod, P.K. / Charman, S.A. / Phillips, M.A.
History
DepositionApr 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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)
B: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,80211
Polymers76,6002
Non-polymers2,2029
Water7,440413
1
A: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5397
Polymers38,3001
Non-polymers1,2396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2634
Polymers38,3001
Non-polymers9633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.530, 89.770, 84.417
Angle α, β, γ (deg.)90.000, 90.036, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydroorotate dehydrogenase (quinone) / DHOdehase / DHOD / DHODase / Dihydroorotate oxidase


Mass: 38299.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB307-0294 / Gene: pyrD, ABBFA_001187 / Plasmid: pET28b / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: B7GZW7, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 5 types, 422 molecules

#2: Chemical ChemComp-OBR / (4R)-7-methyl-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]imidazo[1,2-a]pyrimidin-5-amine


Mass: 350.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11F5N4S / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.28 Å3/Da / Density % sol: 46.2 % / Description: cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.085 M Hepes pH7.5, 8.5% 2-propanol, 17% PEG4000, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97919 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.4→28.2 Å / Num. obs: 133545 / % possible obs: 98.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 17.87 Å2 / Rpim(I) all: 0.021 / Net I/σ(I): 32.4
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 5470 / CC1/2: 0.548 / % possible all: 81.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I65

3i65


Resolution: 1.4→28.2 Å / SU ML: 0.158 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1742 1981 1.51 %
Rwork0.1655 128859 -
obs0.1656 130840 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.93 Å2
Refinement stepCycle: LAST / Resolution: 1.4→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4915 0 148 413 5476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00885217
X-RAY DIFFRACTIONf_angle_d0.98637106
X-RAY DIFFRACTIONf_chiral_restr0.0736812
X-RAY DIFFRACTIONf_plane_restr0.0098902
X-RAY DIFFRACTIONf_dihedral_angle_d14.53041945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.35591220.34047752X-RAY DIFFRACTION82.85
1.43-1.470.31081200.29278705X-RAY DIFFRACTION92.67
1.47-1.520.28231550.25499157X-RAY DIFFRACTION98.09
1.52-1.570.25831210.22479360X-RAY DIFFRACTION99.92
1.57-1.620.19781610.20119378X-RAY DIFFRACTION100
1.62-1.690.20621460.19129370X-RAY DIFFRACTION100
1.69-1.760.17991390.18419329X-RAY DIFFRACTION100
1.76-1.860.21251470.17329348X-RAY DIFFRACTION99.97
1.86-1.970.14951600.15589379X-RAY DIFFRACTION99.97
1.97-2.120.16881460.1539353X-RAY DIFFRACTION99.99
2.12-2.340.16321360.14789426X-RAY DIFFRACTION100
2.34-2.680.17251400.15429418X-RAY DIFFRACTION99.92
2.68-3.370.16631480.15889395X-RAY DIFFRACTION99.94
3.37-28.20.1481400.14899489X-RAY DIFFRACTION99.46
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)
13.56131661428-2.09714757946-2.105012919075.166776437232.110461195134.083041177010.02200881514580.2779010062280.319923114439-0.47099096234-0.0159533259522-0.296336474353-0.1314793154990.2024902474080.007907552245370.244784968412-0.01746466645880.03924084716160.1781897276440.07925891419630.221548050316-9.788462255912.2115423061-56.714447465
21.79248082545-0.2290281491120.08512778224881.76161999875-0.1065041949780.565977521624-0.009950119976310.09088263746060.0162719526289-0.141042024413-0.0238729628312-0.1466544540430.006126043209840.0582819585860.02548381228330.0982144938447-0.002186008709180.02522163971160.09804142545670.01227808887010.19954969709-10.70504866360.822556669135-47.5960759402
33.929962144540.4634986842290.68811090112.56831171709-0.625608132960.598942760422-0.0258849627353-0.139134046871-0.452580877376-0.02700943873820.04323768515090.1398275615710.0428081797394-0.0700594984774-0.03253762887850.1108118674920.009810246155090.01952350930620.09625052425970.01530922576550.260320325544-17.3233691528-10.7219804195-42.4485722856
46.89200884975-4.07764074043-3.602830075348.894443185035.868482576717.86399092428-0.0832026635092-0.199059799876-0.7879120256240.405146218612-0.03614090353820.3432134882970.0322541156173-0.2281729327180.1702199894780.1771126792690.01656504309240.02690306124140.1629515135310.09366181132620.327872593094-17.2039718053-18.8695993408-34.1216425934
52.03192517517-0.5802420622560.3878499831923.21691851312-0.6508558448851.05847065312-0.159494369296-0.397202231505-0.06682728944190.5986434193340.1713375708060.162873750801-0.109029983081-0.0648308699025-0.01476776021910.1545449518970.0310025583530.03207474093390.1846566121690.01069010683080.175393293392-15.50924755241.14442600518-31.0332206666
62.32782022147-0.4109206166370.1004106641372.71956825117-0.7363021529190.594206062576-0.10462423535-0.3056409238130.3398110471870.348343726701-0.0237947593168-0.696894835876-0.1368917337140.1381718958130.1001928014910.1597163806670.00964087577673-0.07285789225050.163489862397-0.02802731557830.34537334228-3.743926149546.40276798086-34.1360377818
73.334329801460.421632720743-1.738492485793.618533657411.117762797361.78018513188-0.2459105872090.0838990193785-0.0904304401812-0.6238883645060.1021305135620.139580202044-0.269279790084-0.1571941423630.1153596821760.624522192687-0.001003196341220.005371834874880.404596670675-0.04160448477680.225388208996.5418059518-25.9600678235-16.3024415278
81.93639836483-0.794527016656-0.5137360985244.392870847990.9350401000092.568037259080.1226792408060.00853831453967-0.00119313659844-0.338304323103-0.112133996427-0.04819965440420.0485482292859-0.1151576953220.008520878204520.384713375387-0.02128049582120.05237695334250.309602041879-0.04068995171970.1442726612387.01313819489-15.6678412424-5.16326125836
90.959529643727-0.84007381716-0.962063617054.075793777651.38406737173.319256541020.196275444997-0.2346609497910.346633135499-0.07902636648010.0747179031004-0.129454582428-0.4726241682330.176590312816-0.2363833867540.382779702869-0.04382781047390.1027316642640.408769679858-0.08622218883180.2463424697366.28243573485-1.19242584694.59758278539
102.19944900587-0.673325472629-1.019848833853.816620976121.272705165382.89083211719-0.104748051287-0.575077440579-0.1140815851630.7881810895170.199578281783-0.6388504382410.6101671131890.501813630101-0.1044746198260.5039438614250.0307486582284-0.05522593717110.487405618111-0.01502565660770.28227949589615.399486851-19.76317547297.37657463588
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 31 )AA1 - 311 - 31
22chain 'A' and (resid 32 through 126 )AA32 - 12632 - 126
33chain 'A' and (resid 127 through 183 )AA127 - 183127 - 173
44chain 'A' and (resid 184 through 205 )AA184 - 205174 - 195
55chain 'A' and (resid 206 through 261 )AA206 - 261196 - 251
66chain 'A' and (resid 262 through 334 )AA262 - 334252 - 324
77chain 'B' and (resid -5 through 31 )BG-5 - 311 - 37
88chain 'B' and (resid 32 through 126 )BG32 - 12638 - 130
99chain 'B' and (resid 127 through 205 )BG127 - 205131 - 195
1010chain 'B' and (resid 206 through 334 )BG206 - 334196 - 324

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