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- PDB-2bsl: Crystal structure of L. lactis dihydroorotate dehydrogense A in c... -

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Basic information

Entry
Database: PDB / ID: 2bsl
TitleCrystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,4-dihydroxybenzoate
ComponentsDIHYDROOROTATE DEHYDROGENASE A
KeywordsOXIDOREDUCTASE / NUCLEOTIDE METABOLISM / DIHYDROOROTATE DEHYDROGENASE / FMN / FLAVOPROTEIN / PYRIMIDINE BIOSYNTHESIS
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
ACETATE ION / 3,4-DIHYDROXYBENZOIC ACID / FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase A (fumarate) / Dihydroorotate dehydrogenase A (fumarate)
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWolfe, A.E. / Hansen, M. / Gattis, S.G. / Hu, Y.-C. / Johansson, E. / Arent, S. / Larsen, S. / Palfey, B.A.
CitationJournal: Biochemistry / Year: 2007
Title: Interaction of Benzoate Pyrimidine Analogues with Class 1A Dihydroorotate Dehydrogenase from Lactococcus Lactis.
Authors: Wolfe, A.E. / Thymark, M. / Gattis, S.G. / Fagan, R.L. / Hu, Y.-C. / Johansson, E. / Arent, S. / Larsen, S. / Palfey, B.A.
History
DepositionMay 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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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)69,7519
Polymers68,4842
Non-polymers1,2677
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.588, 108.160, 66.222
Angle α, β, γ (deg.)90.00, 104.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 128
2112B1 - 128
1212A140 - 312
2212B140 - 312

NCS oper: (Code: given
Matrix: (0.87874, 0.009773, 0.47719), (0.009773, -0.99995, 0.002482), (0.47719, 0.002482, -0.8788)
Vector: -8.4797, 64.399, 32.066)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DIHYDROOROTATE DEHYDROGENASE A / DIHYDROOROTATE DEHYDROGENSE / DHOD A / DIHYDROOROTATE OXIDASE A / DHODEHASE A / DHODASE 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)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P54321, UniProt: A2RJT9*PLUS, EC: 1.3.99.11

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Non-polymers , 6 types, 172 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYSIS: (S)-DIHYDROOROTATE + O2 => OROTATE + H2O2

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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: 2.62 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 17 MG/ML PROTEIN AND 2.6 MM 3, 4-DIOHB HANGING DROPS 2 MICROLITERS OF PROTEIN AND 2 MICROLITERS RESERVOIR: 30 % PEG 6000, 1 MM DTT, 0.2 M SODIUM ACETATE AND 0.1 M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179
DetectorType: MARRESEEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 32557 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.9
Reflection shellResolution: 2.3→2.32 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.6 / % possible all: 62.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OVD

1ovd


Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.805 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1526 5.2 %RANDOM
Rwork0.186 ---
obs0.189 27913 90.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.13 Å2
Baniso -1Baniso -2Baniso -3
1-6.63 Å20 Å2-0.68 Å2
2---4.28 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 85 165 5068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225007
X-RAY DIFFRACTIONr_bond_other_d0.0020.024501
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9926777
X-RAY DIFFRACTIONr_angle_other_deg0.925310557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0475620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025523
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02937
X-RAY DIFFRACTIONr_nbd_refined0.2160.21045
X-RAY DIFFRACTIONr_nbd_other0.2340.25108
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.22763
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2195
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8091.53093
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50524970
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.29431914
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7784.51807
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1759tight positional0.040.05
2776medium positional0.260.5
1759tight thermal0.170.5
2776medium thermal0.662
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 78
Rwork0.25 1526

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