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- PDB-4xq6: CRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENSE from MYCOBACTERI... -

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Basic information

Entry
Database: PDB / ID: 4xq6
TitleCRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENSE from MYCOBACTERIUM TUBERCULOSIS
ComponentsDihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / DIHYDROOROTATE DEHYDROGENSE
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase, class 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 / TIM Barrel ...Dihydroorotate dehydrogenase, class 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase (quinone) / Dihydroorotate dehydrogenase (quinone)
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKishor, C. / Addlagatta, A.
CitationJournal: To Be Published
Title: Crystal structure of Dihydroorotate Dehydrogenase form Mycobacterium Tuberculosis
Authors: Kishor, C. / Addlagatta, A.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_symmetry

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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)74,04510
Polymers72,9312
Non-polymers1,1148
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-66 kcal/mol
Surface area26200 Å2
Unit cell
Length a, b, c (Å)48.335, 106.921, 65.089
Angle α, β, γ (deg.)90.00, 106.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36465.406 Da / Num. of mol.: 2 / Fragment: UNP residues 31-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Strain: H37Ra / Gene: pyrD, MRA_2153
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: A5U4G5, UniProt: P9WHL1*PLUS, dihydroorotate dehydrogenase (quinone)
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 22-27% PEG 3350, 0.1M Bis-Tris pH 5.0, 0.2M Mgcl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 13, 2014
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→27 Å / Num. obs: 39530 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 11.64

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
DENZOdata scaling
MOLREPmodel building
RefinementResolution: 2→23.47 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.257 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1979 5 %RANDOM
Rwork0.17607 ---
obs0.17895 37550 92.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.673 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.01 Å2
2--0.06 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2→23.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 68 213 5028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195025
X-RAY DIFFRACTIONr_bond_other_d0.0010.024913
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.9946863
X-RAY DIFFRACTIONr_angle_other_deg0.989311234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90421.449207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23315780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7511565
X-RAY DIFFRACTIONr_chiral_restr0.1450.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021149
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4612.6472590
X-RAY DIFFRACTIONr_mcbond_other2.462.6462589
X-RAY DIFFRACTIONr_mcangle_it3.623.9533245
X-RAY DIFFRACTIONr_mcangle_other3.6193.9543246
X-RAY DIFFRACTIONr_scbond_it3.0443.0462435
X-RAY DIFFRACTIONr_scbond_other3.0453.0462434
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6984.413611
X-RAY DIFFRACTIONr_long_range_B_refined6.70322.0065955
X-RAY DIFFRACTIONr_long_range_B_other6.66921.9745903
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 77 -
Rwork0.197 1378 -
obs--46.53 %

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