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- PDB-5hy0: orotic acid hydrolase -

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Basic information

Entry
Database: PDB / ID: 5hy0
Titleorotic acid hydrolase
ComponentsRing-opening amidohydrolase
KeywordsHYDROLASE / Toblerone fold / pyrimidine catabolism
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amides / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
Similarity search - Function
Cyanuric acid hydrolase/Barbituras, RU C / Cyanuric acid hydrolase/Barbiturase, RU A / Cyanuric acid hydrolase/Barbiturase / Cyanuric acid hydrolase/Barbiturase, repeating unit B / Cyanuric acid hydrolase/Barbiturase, repeating unit C / Cyanuric acid hydrolase/Barbiturase, repeating unit A / Amidohydrolase ring-opening protein (Amido_AtzD_TrzD) / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cyclic amide hydrolase
Similarity search - Component
Biological speciesFrankia sp. Eul1b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPeat, T.S. / Balotra, S. / Wilding, M. / Newman, J. / Scott, C.
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes.
Authors: Peat, T.S. / Balotra, S. / Wilding, M. / Hartley, C.J. / Newman, J. / Scott, C.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ring-opening amidohydrolase
B: Ring-opening amidohydrolase
C: Ring-opening amidohydrolase
D: Ring-opening amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,5986
Polymers168,4144
Non-polymers1842
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-74 kcal/mol
Surface area52400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.576, 85.661, 87.230
Angle α, β, γ (deg.)96.47, 114.94, 111.77
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA14 - 39034 - 410
21ALAALABB14 - 39034 - 410
12PROPROAA14 - 38934 - 409
22PROPROCC14 - 38934 - 409
13ALAALAAA14 - 39034 - 410
23ALAALADD14 - 39034 - 410
14PROPROBB14 - 38934 - 409
24PROPROCC14 - 38934 - 409
15ALAALABB14 - 39034 - 410
25ALAALADD14 - 39034 - 410
16PROPROCC14 - 38934 - 409
26PROPRODD14 - 38934 - 409

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Ring-opening amidohydrolase


Mass: 42103.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Frankia sp. Eul1b (bacteria) / Plasmid: pET14b variant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: E3JD18, cyanuric acid amidohydrolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein was concentrated to 2.1 mg/mL in 100 mM NaCl and 50 mM HEPES pH 7.5; reservoir was 20% PEG 3350, 0.2 M magnesium acetate, 20 mM HEPES pH 6.8 with the Silver Bullets Bio C1 condition ...Details: Protein was concentrated to 2.1 mg/mL in 100 mM NaCl and 50 mM HEPES pH 7.5; reservoir was 20% PEG 3350, 0.2 M magnesium acetate, 20 mM HEPES pH 6.8 with the Silver Bullets Bio C1 condition of additives; 200 nL of protein added to 90 nL of reservoir and 10 nL of microseeds.
PH range: 6.8 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→46.3 Å / Num. obs: 65127 / % possible obs: 97.5 % / Redundancy: 3.9 % / Net I/σ(I): 24
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.8 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BVQ

4bvq


Resolution: 2.4→41.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 8.021 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.244 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23633 3266 5 %RANDOM
Rwork0.19435 ---
obs0.19644 61420 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.693 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å2-0.6 Å2-0.71 Å2
2---0.28 Å2-0.35 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.4→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10286 0 12 350 10648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910568
X-RAY DIFFRACTIONr_bond_other_d0.010.0210182
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.95914421
X-RAY DIFFRACTIONr_angle_other_deg1.649323350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97551455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35323.792385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13151551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6691574
X-RAY DIFFRACTIONr_chiral_restr0.0890.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112267
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022215
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_it3.2653.5035829
X-RAY DIFFRACTIONr_mcbond_other3.2623.5025828
X-RAY DIFFRACTIONr_mcangle_it5.095.8757281
X-RAY DIFFRACTIONr_mcangle_other5.095.8757282
X-RAY DIFFRACTIONr_scbond_it3.7013.8494739
X-RAY DIFFRACTIONr_scbond_other3.6943.8494739
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.626.3337141
X-RAY DIFFRACTIONr_long_range_B_refined8.54613.89945405
X-RAY DIFFRACTIONr_long_range_B_other8.54613.89945405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A399480.09
12B399480.09
21A405800.1
22C405800.1
31A400600.1
32D400600.1
41B408160.08
42C408160.08
51B404040.07
52D404040.07
61C406760.08
62D406760.08
LS refinement shellResolution: 2.396→2.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 165 -
Rwork0.333 3860 -
obs--81.96 %

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