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- PDB-1jue: 1.8 A resolution structure of native lactococcus lactis dihydroor... -

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Basic information

Entry
Database: PDB / ID: 1jue
Title1.8 A resolution structure of native lactococcus lactis dihydroorotate dehydrogenase A
Componentsdihydroorotate dehydrogenase A
KeywordsOXIDOREDUCTASE / HOMODIMER / ALPHA-BETA BARREL / FLAVOPROTEIN
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase A, chain A, domain 2 / 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 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : ...Dihydroorotate dehydrogenase A, chain A, domain 2 / 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 1. / 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
ACETIC ACID / FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase A (fumarate) / Dihydroorotate dehydrogenase A (fumarate)
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNorager, S. / Arent, S. / Bjornberg, O. / Ottosen, M. / Lo Leggio, L. / Jensen, K.F. / Larsen, S.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function
Authors: Norager, S. / Arent, S. / Bjornberg, O. / Ottosen, M. / Lo Leggio, L. / Jensen, K.F. / Larsen, S.
#1: Journal: Biochemistry / Year: 1997
Title: Active Site of Dihydroorotate Dehydrogenase A from Lactococcus lactis Investigated by Chemical Modification and Mutagenesis
Authors: Bjornberg, O. / Rowland, P. / Larsen, S. / Jensen, K.F.
#2: Journal: Protein Sci. / Year: 1998
Title: The Crystal Structure of Lactococcus lactis Dihydroorotate Dehydrogenase A Complexed with the Enzyme Reaction Product Throws Light on its Enzymatic Function
Authors: Rowland, P. / Bjornberg, O. / Nielsen, F.S. / Jensen, K.F. / Larsen, S.
#3: Journal: Structure / Year: 1997
Title: The Crystal Structure of the Flavin Containing Enzyme Dihydroorotate Dehydrogenase A from Lactococcus lactis
Authors: Rowland, P. / Nielsen, F.S. / Jensen, K.F. / Larsen, S.
#4: Journal: Protein Sci. / Year: 1996
Title: Purification and Characterisation of Dihydroorotate Dehydrogenase A from Lactococcus lactis, Crystallisation and Preliminary X-Ray Diffraction Studies of the Enzyme
Authors: Nielsen, F.S. / Rowland, P. / Larsen, S. / Jensen, K.F.
History
DepositionAug 24, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: dihydroorotate dehydrogenase A
B: dihydroorotate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,02613
Polymers68,4842
Non-polymers1,54211
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-57 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.146, 108.145, 66.019
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains the biological homodimer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein dihydroorotate dehydrogenase A


Mass: 34242.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: PyrD / Plasmid: pUHE23 / Production host: Escherichia coli (E. coli) / Strain (production host): SO6645
References: UniProt: P54321, UniProt: A2RJT9*PLUS, EC: 1.3.3.1

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Non-polymers , 5 types, 618 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6K, Na-acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.9101 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 30, 2000 / Details: Bent mirror
RadiationMonochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.91011
ReflectionResolution: 1.8→20 Å / Num. all: 66564 / Num. obs: 66536 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 22.2
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4393 / % possible all: 97.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LACTOCOCCUS LACTIS DHODA PDB ID 1DOR

1dor


Resolution: 1.8→18 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.198 6529 10.025 %RANDOM
Rwork0.18 ---
obs-64378 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.83 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 102 607 5527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.264 1035 10.3 %
Rwork0.245 11912 -
obs-9052 90.7 %

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