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- PDB-3gz3: Leishmania major Dihydroorotate Dehydrogenase in complex with orotate -

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Basic information

Entry
Database: PDB / ID: 3gz3
TitleLeishmania major Dihydroorotate Dehydrogenase in complex with orotate
ComponentsDihydroorotate dehydrogenase, putative
KeywordsOXIDOREDUCTASE / orotate / DHODH
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / nucleoplasm / cytoplasm
Similarity search - Function
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 domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / Roll ...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 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 / OROTIC ACID / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCordeiro, A.T. / Feliciano, P.R. / Nonato, M.C.
CitationJournal: To be Published
Title: Leismania major dihydroorotate in complex with orotate
Authors: Cordeiro, A.T. / Feliciano, P.R. / Nonato, M.C.
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ncs_dom_lim / 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_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 / _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: Dihydroorotate dehydrogenase, putative
B: Dihydroorotate dehydrogenase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,91210
Polymers76,3192
Non-polymers1,5938
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-32 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.167, 142.167, 69.157
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA1 - 12935 - 163
21METMETLEULEUBB1 - 12935 - 163
12ASPASPFMNFMNAA - C143 - 321177
22ASPASPFMNFMNBB - G143 - 321177

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Components

#1: Protein Dihydroorotate dehydrogenase, putative


Mass: 38159.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LmjF16.0530, pyrD / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q4QEW7, EC: 1.3.3.1
#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-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.2M lithium sulfate, 0.3M ammonium sulfate in 0.1 M sodium citrate tribasic dihydrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.438 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 24, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.438 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 62830 / Num. obs: 62830 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 22.86 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.069 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 3.4 / Num. unique all: 9144 / Rsym value: 0.475 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3gye

3gye


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.532 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.124 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20419 3185 5.1 %RANDOM
Rwork0.17673 ---
obs0.17813 59615 99.9 %-
all-59615 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.313 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4554 0 108 430 5092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224797
X-RAY DIFFRACTIONr_angle_refined_deg1.18226503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59624.428201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91815788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6351524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023620
X-RAY DIFFRACTIONr_nbd_refined0.2040.22934
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23427
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2565
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.215
X-RAY DIFFRACTIONr_mcbond_it0.6341.53072
X-RAY DIFFRACTIONr_mcangle_it1.00324788
X-RAY DIFFRACTIONr_scbond_it1.66532000
X-RAY DIFFRACTIONr_scangle_it2.6624.51708
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2318 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.235
loose thermal0.8710
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 222 -
Rwork0.249 4383 -
obs--99.5 %

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