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- PDB-1j79: Molecular Structure of Dihydroorotase: A Paradigm for Catalysis T... -

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Basic information

Entry
Database: PDB / ID: 1j79
TitleMolecular Structure of Dihydroorotase: A Paradigm for Catalysis Through the Use of a Binuclear Metal Center
Componentsdihydroorotase
KeywordsHYDROLASE / TIM barrel / metalloenzyme / pyrimidine biosynthesis
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
N-CARBAMOYL-L-ASPARTATE / OROTIC ACID / Dihydroorotase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsThoden, J.B. / Phillips Jr., G.N. / Neal, T.M. / Raushel, F.M. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2001
Title: Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center.
Authors: Thoden, J.B. / Phillips Jr., G.N. / Neal, T.M. / Raushel, F.M. / Holden, H.M.
History
DepositionMay 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Based on analysis of electron density, G69 has been modeled as a proline, I119 has been ...SEQUENCE Based on analysis of electron density, G69 has been modeled as a proline, I119 has been modeled as a valine, and N243 has been modeled as a glutamine. K102 is carboxylated.

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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)78,4209
Polymers77,6502
Non-polymers7707
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-172 kcal/mol
Surface area25510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.600, 78.800, 180.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer composed of chains A & B which as deposited represent the actual dimer

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Components

#1: Protein dihydroorotase / dhoase


Mass: 38825.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRC / Production host: Escherichia coli (E. coli) / 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-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 47.86 %
Crystal growTemperature: 277 K / Method: macroseeding / batch / pH: 6
Details: PEG 3400, 2-(N-morpholino)ethanesulfonic acid (MES), potassium chloride, magnesium chloride, N-carbamoyl-DL-aspartate, pH 6.0, macroseeding / batch, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: batch method / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein11
210 mMHEPES11
3180 mM11KCl
410 mMN-carbamoyl-D,L-aspartate11
55 mMdithiothreitol11
66-9 %PEG340012
7100 mMMES12
875 mM12MgCl2
9150 mM12KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.14020, 1.14050, 1.09045, 1.03320
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 7, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.14021
21.14051
31.090451
41.03321
ReflectionResolution: 1.5→99 Å / Num. all: 114211 / Num. obs: 114211 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 41.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.3 / Num. unique all: 10107 / % possible all: 87.5
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 87.5 % / Num. unique obs: 10107

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Processing

Software
NameClassification
SOLVEphasing
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residue 317 of chain A has no density after the CB.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 7904 10 %RANDOM
Rwork0.191 ---
all0.193 79036 --
obs0.193 79036 99 %-
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 39 731 6212
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.15
X-RAY DIFFRACTIONt_bond_d0.012
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor all: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.15
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.01

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