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- PDB-1xge: Dihydroorotase from Escherichia coli: Loop Movement and Cooperati... -

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Basic information

Entry
Database: PDB / ID: 1xge
TitleDihydroorotase from Escherichia coli: Loop Movement and Cooperativity between subunits
ComponentsDihydroorotase
KeywordsHYDROLASE / 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-DOR / N-CARBAMOYL-L-ASPARTATE / Dihydroorotase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Refinement / Resolution: 1.9 Å
AuthorsLee, M. / Chan, C.W. / Guss, J.M. / Christopherson, R.I. / Maher, M.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Dihydroorotase from Escherichia coli: Loop Movement and Cooperativity between Subunits
Authors: Lee, M. / Chan, C.W. / Guss, J.M. / Christopherson, R.I. / Maher, M.J.
History
DepositionSep 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: 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: Refinement description / Category: software
Revision 1.4Oct 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_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)78,1388
Polymers77,5422
Non-polymers5966
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-169 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.582, 78.826, 180.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: pBS + / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / 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-DOR / (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / DIHYDROOROTIC ACID


Mass: 158.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O4
#4: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N2O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.3 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, MES, potassium chloride, magnesium chloride, L-dihydroorotate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 21, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 54214 / Num. obs: 54214 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 31.03 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4883 / % possible all: 83.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: Refinement
Starting model: PDB ENTRY 1J79

1j79


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.381 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.162 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21067 2762 5.1 %RANDOM
Rwork0.16798 ---
all0.17099 54182 --
obs0.17018 51420 92.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.546 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--1.33 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5384 0 27 775 6186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225591
X-RAY DIFFRACTIONr_bond_other_d0.0010.025115
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9577605
X-RAY DIFFRACTIONr_angle_other_deg0.778311841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13123.148270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83115915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5671551
X-RAY DIFFRACTIONr_chiral_restr0.0680.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021169
X-RAY DIFFRACTIONr_nbd_refined0.2030.21206
X-RAY DIFFRACTIONr_nbd_other0.1750.25599
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22741
X-RAY DIFFRACTIONr_nbtor_other0.0810.23255
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2596
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5291.53673
X-RAY DIFFRACTIONr_mcbond_other0.1141.51374
X-RAY DIFFRACTIONr_mcangle_it0.75925591
X-RAY DIFFRACTIONr_scbond_it1.27232289
X-RAY DIFFRACTIONr_scangle_it1.8894.52014
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 167 -
Rwork0.223 3425 -
obs-3425 85.1 %
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)
11.63140.13210.9571.70760.22052.3694-0.04730.0696-0.04440.11330.1005-0.0049-0.09630.202-0.0531-0.22490.0084-0.0239-0.2221-0.0359-0.167630.453639.552280.2608
21.61660.51160.55771.89871.19032.15940.03530.11520.0141-0.03370.0510.01820.2571-0.1669-0.0863-0.1149-0.0296-0.0716-0.1637-0.0169-0.1459.033914.278654.1714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 3464 - 346
2X-RAY DIFFRACTION1AC - D400 - 4011
3X-RAY DIFFRACTION1AG14101
4X-RAY DIFFRACTION2BB4 - 3464 - 346
5X-RAY DIFFRACTION2BE - F400 - 4011
6X-RAY DIFFRACTION2BH24101

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