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- PDB-3oix: Crystal structure of the putative dihydroorotate dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 3oix
TitleCrystal structure of the putative dihydroorotate dehydrogenase from Streptococcus mutans
ComponentsPutative dihydroorotate dehydrogenase; dihydroorotate oxidase
KeywordsOXIDOREDUCTASE / Tim Barrel
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase, class 1 / Dihydroorotate Dehydrogenase A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase ...Dihydroorotate dehydrogenase, class 1 / Dihydroorotate Dehydrogenase A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsLiu, Y. / Gao, Z.Q. / Liu, C.P. / Dong, Y.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of the putative dihydroorotate dehydrogenase from Streptococcus mutans
Authors: Liu, Y. / Gao, Z.-Q. / Liu, C.-P. / Xu, J.-H. / Li, L.-F. / Ji, C.-N. / Su, X.-D. / Dong, Y.-H.
History
DepositionAug 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative dihydroorotate dehydrogenase; dihydroorotate oxidase
B: Putative dihydroorotate dehydrogenase; dihydroorotate oxidase
C: Putative dihydroorotate dehydrogenase; dihydroorotate oxidase
D: Putative dihydroorotate dehydrogenase; dihydroorotate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,07512
Polymers151,8814
Non-polymers2,1948
Water8,881493
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative dihydroorotate dehydrogenase; dihydroorotate oxidase
B: Putative dihydroorotate dehydrogenase; dihydroorotate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0376
Polymers75,9412
Non-polymers1,0974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-34 kcal/mol
Surface area22870 Å2
MethodPISA
3
C: Putative dihydroorotate dehydrogenase; dihydroorotate oxidase
D: Putative dihydroorotate dehydrogenase; dihydroorotate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0376
Polymers75,9412
Non-polymers1,0974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-34 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.126, 158.276, 193.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 3:90 or resseq 94:129 or resseq 137:310 )
211chain B and (resseq 3:90 or resseq 94:129 or resseq 137:310 )
311chain C and (resseq 3:90 or resseq 94:129 or resseq 137:310 )
411chain D and (resseq 3:90 or resseq 94:129 or resseq 137:310 )

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Components

#1: Protein
Putative dihydroorotate dehydrogenase; dihydroorotate oxidase


Mass: 37970.258 Da / Num. of mol.: 4
Mutation: K45(MLY)/K114(MLY)/K137(MLY)/K184(MLY)/K210(MLY)/K251(MLY)/K289(MLY)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: smu.595 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DVA1, EC: 1.3.3.1, dihydroorotate dehydrogenase (quinone)
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.1M MES, 12% PEG 20000, 0.03% dichloromethane, pH 6.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 10, 2010
RadiationMonochromator: double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. all: 62129 / Num. obs: 57164 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 25.8
Reflection shellResolution: 2.399→2.44 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 3.9 / % possible all: 93.5

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DOR

1dor


Resolution: 2.399→33.096 Å / SU ML: 0.39 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 2870 5.09 %random
Rwork0.2015 ---
all0.2038 62129 --
obs0.2038 56428 90.92 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.557 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8207 Å20 Å2-0 Å2
2--2.3502 Å20 Å2
3----6.171 Å2
Refinement stepCycle: LAST / Resolution: 2.399→33.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9631 0 148 493 10272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810027
X-RAY DIFFRACTIONf_angle_d1.17113617
X-RAY DIFFRACTIONf_dihedral_angle_d16.5113783
X-RAY DIFFRACTIONf_chiral_restr0.071507
X-RAY DIFFRACTIONf_plane_restr0.0041735
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2335X-RAY DIFFRACTIONPOSITIONAL
12B2335X-RAY DIFFRACTIONPOSITIONAL0.047
13C2335X-RAY DIFFRACTIONPOSITIONAL0.042
14D2335X-RAY DIFFRACTIONPOSITIONAL0.052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3994-2.44080.32911330.26082194X-RAY DIFFRACTION76
2.4408-2.48520.33711350.25912415X-RAY DIFFRACTION82
2.4852-2.5330.30461390.25972346X-RAY DIFFRACTION82
2.533-2.58460.37411360.25922360X-RAY DIFFRACTION81
2.5846-2.64080.32851470.24692441X-RAY DIFFRACTION84
2.6408-2.70220.28461400.24142493X-RAY DIFFRACTION86
2.7022-2.76980.30051380.24032498X-RAY DIFFRACTION86
2.7698-2.84460.29661150.23312547X-RAY DIFFRACTION87
2.8446-2.92830.27291310.22972618X-RAY DIFFRACTION90
2.9283-3.02270.30811330.22722630X-RAY DIFFRACTION90
3.0227-3.13070.25911580.22532715X-RAY DIFFRACTION92
3.1307-3.25590.27331350.22372830X-RAY DIFFRACTION96
3.2559-3.4040.25211310.20282900X-RAY DIFFRACTION99
3.404-3.58320.24331500.20712879X-RAY DIFFRACTION98
3.5832-3.80740.24311790.20482916X-RAY DIFFRACTION99
3.8074-4.10090.20241530.17282851X-RAY DIFFRACTION96
4.1009-4.51270.19951450.15242900X-RAY DIFFRACTION98
4.5127-5.16350.17881530.13882940X-RAY DIFFRACTION99
5.1635-6.49740.20861390.18943009X-RAY DIFFRACTION99
6.4974-33.09950.21831800.18983076X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 15.5731 Å / Origin y: 2.8392 Å / Origin z: 59.7293 Å
111213212223313233
T0.0605 Å2-0.0539 Å2-0.0059 Å2-0.0256 Å20.0719 Å2--0.0737 Å2
L0.1672 °2-0.1176 °20.0369 °2--0.0991 °20.1451 °2--0.7119 °2
S-0.0413 Å °-0.0183 Å °0.0634 Å °0.0008 Å °-0.043 Å °0.0551 Å °-0.1358 Å °0.1584 Å °-0.0082 Å °
Refinement TLS groupSelection details: all

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