PDB-5hy4: Structure-function analysis of functionally diverse members of th...

ID or keywords:

Entry

Database: PDB / ID: 5hy4

Title

Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes

Components

Ring-opening amidohydrolase

Keywords

HYDROLASE / 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

Biological species

Frankia sp. Eul1b (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.56 Å

Authors

Peat, T.S. / Balotra, S. / Wilding, M. / Newman, J. / Scott, C.

Citation

Journal: 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

Deposition	Feb 1, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 15, 2017	Group: Database references
Revision 1.2	Apr 26, 2017	Group: Database references
Revision 1.3	Sep 27, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hy4.cif.gz	496.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5hy4.ent.gz	405 KB	Display	PDB format
PDBx/mmJSON format	5hy4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5hy4_validation.pdf.gz	521.2 KB	Display	wwPDB validaton report
Full document	5hy4_full_validation.pdf.gz	555.1 KB	Display
Data in XML	5hy4_validation.xml.gz	92.9 KB	Display
Data in CIF	5hy4_validation.cif.gz	128.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hy/5hy4 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hy4	HTTPS FTP

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Related structure data

Related structure data	5hweC 5hxuC 5hxzC 5hy0SC 5hy1C 5hy2C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5hy0-d 6dhj-2 5hy2-1 4hm1-1 3gzx-1 1o7g-1 3mbh-d 3b9t-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ring-opening amidohydrolase

B: Ring-opening amidohydrolase

C: Ring-opening amidohydrolase

D: Ring-opening amidohydrolase

E: Ring-opening amidohydrolase

F: Ring-opening amidohydrolase

G: Ring-opening amidohydrolase

H: Ring-opening amidohydrolase

337 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ring-opening amidohydrolase

B: Ring-opening amidohydrolase

C: Ring-opening amidohydrolase

D: Ring-opening amidohydrolase

defined by author&software
168 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Ring-opening amidohydrolase

F: Ring-opening amidohydrolase

G: Ring-opening amidohydrolase

H: Ring-opening amidohydrolase

defined by author&software
168 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.762, 105.799, 299.127
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	PRO	PRO	A	A	14 - 389	34 - 409
2	1	ARG	ARG	PRO	PRO	B	B	14 - 389	34 - 409
1	2	ARG	ARG	LEU	LEU	A	A	14 - 388	34 - 408
2	2	ARG	ARG	LEU	LEU	C	C	14 - 388	34 - 408
1	3	ARG	ARG	ARG	ARG	A	A	14 - 387	34 - 407
2	3	ARG	ARG	ARG	ARG	D	D	14 - 387	34 - 407
1	4	ARG	ARG	LEU	LEU	A	A	14 - 388	34 - 408
2	4	ARG	ARG	LEU	LEU	E	E	14 - 388	34 - 408
1	5	ARG	ARG	ALA	ALA	A	A	14 - 390	34 - 410
2	5	ARG	ARG	ALA	ALA	F	F	14 - 390	34 - 410
1	6	TYR	TYR	ARG	ARG	A	A	15 - 386	35 - 406
2	6	TYR	TYR	ARG	ARG	G	G	15 - 386	35 - 406
1	7	ARG	ARG	PRO	PRO	A	A	14 - 389	34 - 409
2	7	ARG	ARG	PRO	PRO	H	H	14 - 389	34 - 409
1	8	ARG	ARG	LEU	LEU	B	B	14 - 388	34 - 408
2	8	ARG	ARG	LEU	LEU	C	C	14 - 388	34 - 408
1	9	ARG	ARG	ARG	ARG	B	B	14 - 387	34 - 407
2	9	ARG	ARG	ARG	ARG	D	D	14 - 387	34 - 407
1	10	ARG	ARG	LEU	LEU	B	B	14 - 388	34 - 408
2	10	ARG	ARG	LEU	LEU	E	E	14 - 388	34 - 408
1	11	ARG	ARG	PRO	PRO	B	B	14 - 389	34 - 409
2	11	ARG	ARG	PRO	PRO	F	F	14 - 389	34 - 409
1	12	TYR	TYR	ARG	ARG	B	B	15 - 386	35 - 406
2	12	TYR	TYR	ARG	ARG	G	G	15 - 386	35 - 406
1	13	ARG	ARG	PRO	PRO	B	B	14 - 389	34 - 409
2	13	ARG	ARG	PRO	PRO	H	H	14 - 389	34 - 409
1	14	ARG	ARG	ARG	ARG	C	C	14 - 387	34 - 407
2	14	ARG	ARG	ARG	ARG	D	D	14 - 387	34 - 407
1	15	ARG	ARG	LEU	LEU	C	C	14 - 388	34 - 408
2	15	ARG	ARG	LEU	LEU	E	E	14 - 388	34 - 408
1	16	ARG	ARG	LEU	LEU	C	C	14 - 388	34 - 408
2	16	ARG	ARG	LEU	LEU	F	F	14 - 388	34 - 408
1	17	TYR	TYR	ARG	ARG	C	C	15 - 386	35 - 406
2	17	TYR	TYR	ARG	ARG	G	G	15 - 386	35 - 406
1	18	ARG	ARG	LEU	LEU	C	C	14 - 388	34 - 408
2	18	ARG	ARG	LEU	LEU	H	H	14 - 388	34 - 408
1	19	ARG	ARG	ARG	ARG	D	D	14 - 387	34 - 407
2	19	ARG	ARG	ARG	ARG	E	E	14 - 387	34 - 407
1	20	ARG	ARG	ARG	ARG	D	D	14 - 387	34 - 407
2	20	ARG	ARG	ARG	ARG	F	F	14 - 387	34 - 407
1	21	TYR	TYR	ARG	ARG	D	D	15 - 386	35 - 406
2	21	TYR	TYR	ARG	ARG	G	G	15 - 386	35 - 406
1	22	ARG	ARG	ARG	ARG	D	D	14 - 387	34 - 407
2	22	ARG	ARG	ARG	ARG	H	H	14 - 387	34 - 407
1	23	ARG	ARG	LEU	LEU	E	E	14 - 388	34 - 408
2	23	ARG	ARG	LEU	LEU	F	F	14 - 388	34 - 408
1	24	TYR	TYR	ARG	ARG	E	E	15 - 386	35 - 406
2	24	TYR	TYR	ARG	ARG	G	G	15 - 386	35 - 406
1	25	ARG	ARG	LEU	LEU	E	E	14 - 388	34 - 408
2	25	ARG	ARG	LEU	LEU	H	H	14 - 388	34 - 408
1	26	TYR	TYR	ARG	ARG	F	F	15 - 386	35 - 406
2	26	TYR	TYR	ARG	ARG	G	G	15 - 386	35 - 406
1	27	ARG	ARG	PRO	PRO	F	F	14 - 389	34 - 409
2	27	ARG	ARG	PRO	PRO	H	H	14 - 389	34 - 409
1	28	TYR	TYR	ARG	ARG	G	G	15 - 386	35 - 406
2	28	TYR	TYR	ARG	ARG	H	H	15 - 386	35 - 406

NCS ensembles :

#1: Protein	Ring-opening amidohydrolase Mass: 42103.465 Da / Num. of mol.: 8 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.: 256 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 43.55 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein was concentrated to 4.2 mg/mL; reservoir was 20% PEG 3350 and 0.2 M magnesium acetate at 8 C; drops were 150 nL protein plus 150 nL reservoir.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.56→46.7 Å / Num. obs: 95206 / % possible obs: 99.5 % / Redundancy: 7.5 % / Net I/σ(I): 12.5
Reflection shell	Resolution: 2.56→2.6 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.8 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HY0

5hy0

Resolution: 2.56→46.7 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.896 / SU B: 12.599 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.8 / ESU R Free: 0.322 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26343	4666	4.9 %	RANDOM
R_work	0.22943	-	-	-
obs	0.2311	90462	99.38 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 53.899 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.58 Å²	-0 Å²	-0 Å²
2-	-	-1.37 Å²	0 Å²
3-	-	-	1.95 Å²

Refinement step

Cycle: 1 / Resolution: 2.56→46.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19446	0	0	256	19702

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	19900
X-RAY DIFFRACTION	r_bond_other_d	0.012	0.02	19148
X-RAY DIFFRACTION	r_angle_refined_deg	1.522	1.957	27160
X-RAY DIFFRACTION	r_angle_other_deg	2.097	3	43860
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.244	5	2762
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.808	23.971	700
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.658	15	2862
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.431	15	126
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	3309
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	23098
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	4124
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.378	5.471	11111
X-RAY DIFFRACTION	r_mcbond_other	4.377	5.471	11110
X-RAY DIFFRACTION	r_mcangle_it	6.846	8.174	13852
X-RAY DIFFRACTION	r_mcangle_other	6.846	8.174	13853
X-RAY DIFFRACTION	r_scbond_it	3.923	5.609	8789
X-RAY DIFFRACTION	r_scbond_other	3.923	5.609	8790
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.243	8.342	13309
X-RAY DIFFRACTION	r_long_range_B_refined	11.373	50.613	84898
X-RAY DIFFRACTION	r_long_range_B_other	11.375	50.63	84818
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	40028	0.09
1	2	B	40028	0.09
2	1	A	37114	0.11
2	2	C	37114	0.11
3	1	A	35864	0.1
3	2	D	35864	0.1
4	1	A	38500	0.09
4	2	E	38500	0.09
5	1	A	37508	0.1
5	2	F	37508	0.1
6	1	A	35174	0.13
6	2	G	35174	0.13
7	1	A	36544	0.08
7	2	H	36544	0.08
8	1	B	37222	0.11
8	2	C	37222	0.11
9	1	B	36036	0.1
9	2	D	36036	0.1
10	1	B	38426	0.09
10	2	E	38426	0.09
11	1	B	37476	0.11
11	2	F	37476	0.11
12	1	B	35142	0.13
12	2	G	35142	0.13
13	1	B	36910	0.08
13	2	H	36910	0.08
14	1	C	35344	0.1
14	2	D	35344	0.1
15	1	C	37546	0.1
15	2	E	37546	0.1
16	1	C	35834	0.12
16	2	F	35834	0.12
17	1	C	34064	0.12
17	2	G	34064	0.12
18	1	C	36108	0.1
18	2	H	36108	0.1
19	1	D	36058	0.09
19	2	E	36058	0.09
20	1	D	34602	0.11
20	2	F	34602	0.11
21	1	D	32930	0.13
21	2	G	32930	0.13
22	1	D	35394	0.09
22	2	H	35394	0.09
23	1	E	36848	0.1
23	2	F	36848	0.1
24	1	E	34578	0.12
24	2	G	34578	0.12
25	1	E	36782	0.08
25	2	H	36782	0.08
26	1	F	33176	0.14
26	2	G	33176	0.14
27	1	F	34678	0.1
27	2	H	34678	0.1
28	1	G	32648	0.12
28	2	H	32648	0.12

LS refinement shell

Resolution: 2.56→2.626 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	337	-
R_work	0.333	6593	-
obs	-	-	99.17 %

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