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- PDB-5ue9: WT DHODB with orotate bound -

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Basic information

Entry
Database: PDB / ID: 5ue9
TitleWT DHODB with orotate bound
Components(Dihydroorotate ...) x 2
KeywordsOXIDOREDUCTASE / orotate / pyrimidine biosynthesis / FeS cluster / electron transfer / dehydrogenase / protein engineering
Function / homology
Function and homology information


dihydroorotate dehydrogenase (NAD+) / dihydroorotate dehydrogenase (NAD+) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / electron transfer activity / metal ion binding / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase B (pyrk subunit); domain 3 / Dihydroorotate dehydrogenase, electron transfer subunit / Dihydroorotate dehydrogenase electron transfer subunit / Dihydroorotate dehydrogenase, class 1B / Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate dehydrogenase, class 1/ 2 ...Dihydroorotate dehydrogenase B (pyrk subunit); domain 3 / Dihydroorotate dehydrogenase, electron transfer subunit / Dihydroorotate dehydrogenase electron transfer subunit / Dihydroorotate dehydrogenase, class 1B / Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Ribbon / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / OROTIC ACID / : / : / Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit / Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsPompeu, Y.A. / Stewart, J.D.
CitationJournal: to be published
Title: Isoleucine 74 Plays a Key Role in Controlling Electron Transfer Between Lactococcus lactis Dihydroorotate Dehydrogenase 1B Subunits
Authors: Pompeu, Y.A. / Stewart, J.D.
History
DepositionDec 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase
B: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
D: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
C: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,77815
Polymers122,4104
Non-polymers3,36711
Water3,585199
1
A: Dihydroorotate dehydrogenase
B: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
hetero molecules

A: Dihydroorotate dehydrogenase
B: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,81316
Polymers122,4104
Non-polymers3,40312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area15560 Å2
ΔGint-126 kcal/mol
Surface area40590 Å2
MethodPISA
2
D: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
C: Dihydroorotate dehydrogenase
hetero molecules

D: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
C: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,74214
Polymers122,4104
Non-polymers3,33210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area15680 Å2
ΔGint-114 kcal/mol
Surface area39880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.207, 151.911, 214.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 134 or resid 136 through 309))
21(chain C and (resid 5 through 134 or resid 136 through 309))
12(chain B and (resid 1 through 9 or (resid 10...
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNSERSER(chain A and (resid 5 through 134 or resid 136 through 309))AA5 - 1341 - 130
121PROPROSERSER(chain A and (resid 5 through 134 or resid 136 through 309))AA136 - 309132 - 305
211ASNASNSERSER(chain C and (resid 5 through 134 or resid 136 through 309))CD5 - 1341 - 130
221PROPROSERSER(chain C and (resid 5 through 134 or resid 136 through 309))CD136 - 309132 - 305
112METMETTHRTHR(chain B and (resid 1 through 9 or (resid 10...BB1 - 91 - 9
122ILEILEVALVAL(chain B and (resid 1 through 9 or (resid 10...BB10 - 1110 - 11
132METMETLEULEU(chain B and (resid 1 through 9 or (resid 10...BB1 - 2621 - 262
142METMETLEULEU(chain B and (resid 1 through 9 or (resid 10...BB1 - 2621 - 262
152METMETLEULEU(chain B and (resid 1 through 9 or (resid 10...BB1 - 2621 - 262
162METMETLEULEU(chain B and (resid 1 through 9 or (resid 10...BB1 - 2621 - 262
172METMETLEULEU(chain B and (resid 1 through 9 or (resid 10...BB1 - 2621 - 262
182METMETLEULEU(chain B and (resid 1 through 9 or (resid 10...BB1 - 2621 - 262
212METMETLEULEUchain DDC1 - 2621 - 262

NCS ensembles :
ID
1
2

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Components

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Dihydroorotate ... , 2 types, 4 molecules ACBD

#1: Protein Dihydroorotate dehydrogenase / / DHOdehase


Mass: 32342.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: pyrD, NCDO895_2365 / Plasmid: pET-22(b)+ / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0V8EUT4, UniProt: Q9CFW8*PLUS, dihydroorotate dehydrogenase (NAD+)
#2: Protein Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit / Dihydroorotate oxidase B / electron transfer subunit


Mass: 28862.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: pyrK, NCDO895_2366 / Plasmid: pet 22b+ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0V8EGX5, UniProt: Q9CFW7*PLUS

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Non-polymers , 7 types, 210 molecules

#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M NaAcetate pH 4, PEG 4k 12% w/v, glycerol 3% v/v

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.72→53 Å / Num. obs: 34552 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 50.8 Å2 / Rsym value: 0.09 / Net I/σ(I): 7.34

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_2621refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EP2

1ep2


Resolution: 2.72→50.389 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.04
RfactorNum. reflection% reflection
Rfree0.2543 1731 5.03 %
Rwork0.1949 --
obs0.198 34435 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.43 Å2 / Biso mean: 42.4345 Å2 / Biso min: 17.57 Å2
Refinement stepCycle: final / Resolution: 2.72→50.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8541 0 211 199 8951
Biso mean--37.28 37.14 -
Num. residues----1135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098913
X-RAY DIFFRACTIONf_angle_d1.21412100
X-RAY DIFFRACTIONf_chiral_restr0.0641400
X-RAY DIFFRACTIONf_plane_restr0.0081530
X-RAY DIFFRACTIONf_dihedral_angle_d13.515411
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2848X-RAY DIFFRACTION10.555TORSIONAL
12C2848X-RAY DIFFRACTION10.555TORSIONAL
21B2493X-RAY DIFFRACTION10.555TORSIONAL
22D2493X-RAY DIFFRACTION10.555TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7201-2.80010.3911440.29022772291699
2.8001-2.89050.32871460.2562767291399
2.8905-2.99380.29211560.2552729288599
2.9938-3.11370.31711240.23792747287198
3.1137-3.25530.33051470.2322708285597
3.2553-3.42690.3151400.23012713285396
3.4269-3.64160.30981500.2032691284196
3.6416-3.92270.25731440.1922721286597
3.9227-4.31720.2031420.16952711285396
4.3172-4.94150.1911460.14292679282595
4.9415-6.22390.23321370.17552697283494
6.2239-50.3980.20261550.17632769292493

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