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- PDB-4yiw: DIHYDROOROTASE FROM BACILLUS ANTHRACIS WITH SUBSTRATE BOUND -

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Basic information

Entry
Database: PDB / ID: 4yiw
TitleDIHYDROOROTASE FROM BACILLUS ANTHRACIS WITH SUBSTRATE BOUND
ComponentsDihydroorotase
KeywordsHYDROLASE
Function / homology
Function and homology information


allantoinase activity / dihydroorotase / purine nucleobase catabolic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / zinc ion binding / cytoplasm
Similarity search - Function
Dihydroorotase / : / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related ...Dihydroorotase / : / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-CARBAMOYL-L-ASPARTATE / Dihydroorotase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLei, H. / Santarsiero, B.D. / Rice, A.J. / Lee, H. / Johnson, M.E.
CitationJournal: Bioorg.Med.Chem. / Year: 2016
Title: Ca-asp bound X-ray structure and inhibition of Bacillus anthracis dihydroorotase (DHOase).
Authors: Rice, A.J. / Lei, H. / Santarsiero, B.D. / Lee, H. / Johnson, M.E.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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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)99,1388
Polymers98,5242
Non-polymers6146
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-187 kcal/mol
Surface area32300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.183, 81.676, 104.529
Angle α, β, γ (deg.)90.00, 100.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydroorotase / DHOase


Mass: 49262.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: pyrC, BA_4027, GBAA_4027, BAS3739 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q81WF0, dihydroorotase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


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


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: BIS-tris, PEG3350 / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.33→19.72 Å / Num. obs: 32369 / % possible obs: 89.5 % / Redundancy: 3.44 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.05
Reflection shellResolution: 2.33→2.47 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MPG

3mpg


Resolution: 2.45→19.72 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.897 / SU B: 14.054 / SU ML: 0.291 / Cross valid method: THROUGHOUT / σ(F): 1.38 / ESU R: 1.049 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26464 1521 5 %RANDOM
Rwork0.20566 ---
obs0.20862 28978 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.11 Å2
2--0.12 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.45→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6497 0 28 310 6835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196639
X-RAY DIFFRACTIONr_bond_other_d0.0020.026416
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9638985
X-RAY DIFFRACTIONr_angle_other_deg0.733314824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4595848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51525.208288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5861530
X-RAY DIFFRACTIONr_chiral_restr0.0570.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0474.1723398
X-RAY DIFFRACTIONr_mcbond_other1.0474.1723397
X-RAY DIFFRACTIONr_mcangle_it1.8396.2544244
X-RAY DIFFRACTIONr_mcangle_other1.8396.2554245
X-RAY DIFFRACTIONr_scbond_it0.8844.33241
X-RAY DIFFRACTIONr_scbond_other0.8844.3013242
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5976.3864742
X-RAY DIFFRACTIONr_long_range_B_refined3.89532.1657303
X-RAY DIFFRACTIONr_long_range_B_other3.72932.1857183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 120 -
Rwork0.383 2108 -
obs--98.63 %

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