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- PDB-2z25: Thr110Val dihydroorotase from E. coli -

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Basic information

Entry
Database: PDB / ID: 2z25
TitleThr110Val dihydroorotase from E. coli
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 / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLee, M. / Maher, M.J. / Guss, J.M.
CitationJournal: Biochemistry / Year: 2007
Title: Kinetic and Structural Analysis of Mutant Escherichia coli Dihydroorotases: A Flexible Loop Stabilizes the Transition State
Authors: Lee, M. / Maher, M.J. / Christopherson, R.I. / Guss, J.M.
History
DepositionMay 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / 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 / _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 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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)78,1348
Polymers77,5382
Non-polymers5966
Water12,034668
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.447, 78.968, 180.534
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: 38769.109 Da / Num. of mol.: 2 / Mutation: T110V
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-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


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 17% PEG 3350, 0.1M MES, 75mM MgCl2, 0.15M KCl, pH 6.25, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→40 Å / Num. all: 60822 / Num. obs: 60822 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.3
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4334 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XGE

1xge


Resolution: 1.87→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.516 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18482 3091 5.1 %RANDOM
Rwork0.14726 ---
obs0.14914 60822 98.43 %-
all-60822 --
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: 25.814 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2--0.74 Å20 Å2
3---0.09 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.87→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5384 0 27 668 6079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225527
X-RAY DIFFRACTIONr_bond_other_d0.0010.025047
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9587523
X-RAY DIFFRACTIONr_angle_other_deg0.815311672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20823.231260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67415885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5621547
X-RAY DIFFRACTIONr_chiral_restr0.0740.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021149
X-RAY DIFFRACTIONr_nbd_refined0.2080.21118
X-RAY DIFFRACTIONr_nbd_other0.1780.25351
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22721
X-RAY DIFFRACTIONr_nbtor_other0.0810.23158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2456
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.220
X-RAY DIFFRACTIONr_mcbond_it3.22743666
X-RAY DIFFRACTIONr_mcbond_other1.05641375
X-RAY DIFFRACTIONr_mcangle_it3.70965564
X-RAY DIFFRACTIONr_scbond_it5.39982234
X-RAY DIFFRACTIONr_scangle_it7.122101958
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 218 -
Rwork0.176 4116 -
obs-4334 96.18 %
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)
11.57030.13850.46671.21710.07451.16920.0314-0.0316-0.02730.10280.00880.0006-0.01750.0647-0.0402-0.14870.0045-0.0177-0.1703-0.02-0.155430.472739.70580.3261
21.37820.30340.37731.58780.84161.68490.01210.0557-0.01660.01530.0385-0.04570.1418-0.1466-0.0506-0.1111-0.0094-0.0352-0.1097-0.0267-0.12718.998214.466754.2607
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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