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- PDB-5hy2: Structure-function analysis of functionally diverse members of th... -

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Basic information

Entry
Database: PDB / ID: 5hy2
TitleStructure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes
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: 2.6 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ring-opening amidohydrolase
B: Ring-opening amidohydrolase


Theoretical massNumber of molelcules
Total (without water)84,2072
Polymers84,2072
Non-polymers00
Water55831
1
A: Ring-opening amidohydrolase
B: Ring-opening amidohydrolase

A: Ring-opening amidohydrolase
B: Ring-opening amidohydrolase


Theoretical massNumber of molelcules
Total (without water)168,4144
Polymers168,4144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8530 Å2
ΔGint-78 kcal/mol
Surface area49740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.297, 72.750, 133.054
Angle α, β, γ (deg.)90.00, 92.22, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 14 - 390 / Label seq-ID: 34 - 410

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ring-opening amidohydrolase


Mass: 42103.465 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein was at 2.7 mg/mL with added atrazine; reservoir was 22% PEG 3350, 86 mM sodium acetate; drops were 150 nL protein plus 140 nL reservoir plus 10 nL microseeds.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9707 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9707 Å / Relative weight: 1
ReflectionResolution: 2.6→46.6 Å / Num. obs: 27567 / % possible obs: 99.9 % / Redundancy: 7.5 % / Net I/σ(I): 14
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HY0

5hy0


Resolution: 2.6→41.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.081 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.273 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24123 1354 4.9 %RANDOM
Rwork0.20217 ---
obs0.20403 26209 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-1.97 Å2
2--4.35 Å20 Å2
3----3.25 Å2
Refinement stepCycle: 1 / Resolution: 2.6→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 0 31 4750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194835
X-RAY DIFFRACTIONr_bond_other_d0.010.024683
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9596598
X-RAY DIFFRACTIONr_angle_other_deg1.474310732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8415665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99723.793174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88815699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9621532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215605
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021015
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_it4.595.3732675
X-RAY DIFFRACTIONr_mcbond_other4.5875.3712674
X-RAY DIFFRACTIONr_mcangle_it7.2038.0263335
X-RAY DIFFRACTIONr_mcangle_other7.2038.0283336
X-RAY DIFFRACTIONr_scbond_it4.6445.7012160
X-RAY DIFFRACTIONr_scbond_other4.6435.7032161
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2418.4243264
X-RAY DIFFRACTIONr_long_range_B_refined11.56450.01220195
X-RAY DIFFRACTIONr_long_range_B_other11.56550.01520195
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 36002 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 125 -
Rwork0.334 1875 -
obs--98.43 %

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