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- PDB-2eg7: The crystal structure of E. coli dihydroorotase complexed with HDDP -

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Basic information

Entry
Database: PDB / ID: 2eg7
TitleThe crystal structure of E. coli dihydroorotase complexed with HDDP
ComponentsDihydroorotase
KeywordsHYDROLASE / amidohydrolase / TIM barrel
Function / homology
Function and homology information


dihydroorotase / pyrimidine nucleotide biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / protein homodimerization activity / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Dihydroorotase homodimeric type / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Amidohydrolase family / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-OTD / Dihydroorotase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Refinement / Resolution: 2 Å
AuthorsLee, M. / Maher, M.J. / Guss, J.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structures of Ligand-free and Inhibitor Complexes of Dihydroorotase from Escherichia coli: Implications for Loop Movement in Inhibitor Design
Authors: Lee, M. / Chan, C.W. / Graham, S.C. / Christopherson, R.I. / Guss, J.M. / Maher, M.J.
History
DepositionFeb 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotase
B: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1768
Polymers77,5422
Non-polymers6346
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-181 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.585, 79.628, 180.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains one copy of the biological dimer.

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Components

#1: Protein Dihydroorotase / DHOase


Mass: 38771.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRC / Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / Strain (production host): X7014a / References: UniProt: P05020, dihydroorotase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OTD / 2-OXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4,6-DICARBOXYLIC ACID / HDDP


Mass: 186.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-20% PEG 3350, 0.1M MES, 75mM MgCl2, 150mM KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2006 / Details: Bending magnet
RadiationMonochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 51220 / Num. obs: 46251 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3201 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Refinement
Starting model: PDB entry 1XGE

1xge


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.14 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23533 2384 5.2 %RANDOM
Rwork0.17989 ---
obs0.18272 46251 90.3 %-
all-51220 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.045 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å20 Å2
2--1.9 Å20 Å2
3----3.79 Å2
Refine analyzeLuzzati coordinate error obs: 0.199 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5388 0 30 346 5764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225528
X-RAY DIFFRACTIONr_bond_other_d0.0010.025036
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9597524
X-RAY DIFFRACTIONr_angle_other_deg0.844311650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4325686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8423.333258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35615889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1131545
X-RAY DIFFRACTIONr_chiral_restr0.0830.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021139
X-RAY DIFFRACTIONr_nbd_refined0.2030.21137
X-RAY DIFFRACTIONr_nbd_other0.1810.25308
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22685
X-RAY DIFFRACTIONr_nbtor_other0.0830.23124
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2301
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0850.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.27
X-RAY DIFFRACTIONr_mcbond_it0.7421.54420
X-RAY DIFFRACTIONr_mcbond_other0.1491.51375
X-RAY DIFFRACTIONr_mcangle_it0.86925565
X-RAY DIFFRACTIONr_scbond_it1.55432385
X-RAY DIFFRACTIONr_scangle_it2.2974.51958
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 163 -
Rwork0.286 3201 -
obs-3201 91.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.67690.06260.68011.7926-0.45832.4717-0.0388-0.0277-0.04250.12080.0490.024-0.10770.0454-0.0102-0.16390.0142-0.0165-0.1704-0.036-0.15230.395440.288180.355
21.6340.33950.7061.70891.04492.9850.02170.00170.02270.00820.0562-0.05760.1815-0.4307-0.0779-0.0672-0.0606-0.0468-0.0333-0.0078-0.1349.026114.589254.2782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 3464 - 346
2X-RAY DIFFRACTION2BB4 - 3464 - 346

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