PDB-4zuq: Crystal structure of acetylpolyamine amidohydrolase from Mycoplan...

ID or keywords:

Entry

Database: PDB / ID: 4zuq

Title

Crystal structure of acetylpolyamine amidohydrolase from Mycoplana ramosa in complex with a hydroxamate inhibitor

Components

Acetylpolyamine aminohydrolase

Keywords

Hydrolase/Hydrolase inhibitor / acetylpolyamine amidohydrolase / arginase fold / enzyme-inhibitor complex /

polyamine / Hydrolase-Hydrolase inhibitor complex

Function / homology

Function and homology information

acetylspermidine deacetylase /

acetylspermidine deacetylase activity /

acetylputrescine deacetylase /

acetylputrescine deacetylase activity /

Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides /

histone deacetylase activity /

metal ion binding
Similarity search - Function

Biological species

Mycoplana ramosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.22 Å

Authors

Decroos, C. / Christianson, D.W.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2015
Title: Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase.
Authors: Decroos, C. / Christianson, D.W.

History

Deposition	May 17, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 5, 2015	Group: Database references
Revision 1.2	Aug 12, 2015	Group: Database references
Revision 1.3	Sep 13, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zuq.cif.gz	301.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4zuq.ent.gz	242 KB	Display	PDB format
PDBx/mmJSON format	4zuq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zu/4zuq ftp://data.pdbj.org/pub/pdb/validation_reports/zu/4zuq	HTTPS FTP

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Related structure data

Related structure data	4zumC 4zunC 4zuoC 4zupC 4zurC 3q9bS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3q9f-2 3q9e-3 3q9e-6 3q9b-4 3q9f-3 3q9b-5 3q9e-2 3q9c-3 3q9b-6 3q9f-1 4zur-d 3q9b-3 3q9b-1 3q9b-2 3q9c-1 3q9e-1 3q9f-5 3q9c-6 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: Acetylpolyamine aminohydrolase

B: Acetylpolyamine aminohydrolase

hetero molecules

73.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	44.917, 120.511, 64.408
Angle α, β, γ (deg.)	90.00, 96.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Acetylpolyamine aminohydrolase Mass: 36369.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplana ramosa (bacteria) / Gene: aphA, aph / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q48935

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Non-polymers , 6 types, 954 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-6XA / 6-amino-N-hydroxyhexanamide Mass: 146.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄N₂O₂
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 940 / 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: 2.38 Å³/Da / Density % sol: 48.3 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M LiCl, 20% (w/v) PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 1.22→41.8 Å / Num. obs: 199748 / % possible obs: 99.4 % / Redundancy: 7 % / R_merge(I) obs: 0.079 / Net I/σ(I): 21.5
Reflection shell	Resolution: 1.22→1.26 Å / Redundancy: 7 % / R_merge(I) obs: 0.525 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	dev_1833	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3Q9B

3q9b

Resolution: 1.22→41.8 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 13.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.152	10060	5.04 %
R_work	0.1374	-	-
obs	0.1381	199693	99.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.22→41.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5121	0	52	940	6113

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5774
X-RAY DIFFRACTION	f_angle_d	1.331	7890
X-RAY DIFFRACTION	f_dihedral_angle_d	12.983	2085
X-RAY DIFFRACTION	f_chiral_restr	0.087	825
X-RAY DIFFRACTION	f_plane_restr	0.007	1067

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.2202-1.234	0.2282	347	0.2179	6129	X-RAY DIFFRACTION	97
1.234-1.2485	0.2094	328	0.1971	6391	X-RAY DIFFRACTION	100
1.2485-1.2638	0.1916	330	0.1846	6357	X-RAY DIFFRACTION	100
1.2638-1.2798	0.1869	358	0.1703	6309	X-RAY DIFFRACTION	100
1.2798-1.2966	0.179	299	0.1636	6396	X-RAY DIFFRACTION	100
1.2966-1.3144	0.1861	336	0.153	6396	X-RAY DIFFRACTION	100
1.3144-1.3331	0.1662	350	0.148	6249	X-RAY DIFFRACTION	100
1.3331-1.353	0.1743	359	0.1474	6392	X-RAY DIFFRACTION	100
1.353-1.3742	0.1556	325	0.147	6327	X-RAY DIFFRACTION	100
1.3742-1.3967	0.1684	325	0.1421	6397	X-RAY DIFFRACTION	100
1.3967-1.4208	0.166	368	0.145	6260	X-RAY DIFFRACTION	100
1.4208-1.4466	0.1541	356	0.1415	6380	X-RAY DIFFRACTION	100
1.4466-1.4745	0.1699	338	0.141	6311	X-RAY DIFFRACTION	100
1.4745-1.5046	0.1422	332	0.1327	6338	X-RAY DIFFRACTION	99
1.5046-1.5373	0.1417	340	0.1292	6262	X-RAY DIFFRACTION	99
1.5373-1.573	0.1405	328	0.1255	6237	X-RAY DIFFRACTION	98
1.573-1.6124	0.1457	356	0.1216	6188	X-RAY DIFFRACTION	98
1.6124-1.656	0.1499	316	0.1255	6235	X-RAY DIFFRACTION	98
1.656-1.7047	0.1398	323	0.1226	6242	X-RAY DIFFRACTION	98
1.7047-1.7597	0.1365	335	0.1272	6219	X-RAY DIFFRACTION	98
1.7597-1.8226	0.1409	353	0.1314	6240	X-RAY DIFFRACTION	98
1.8226-1.8956	0.1443	315	0.1334	6353	X-RAY DIFFRACTION	99
1.8956-1.9819	0.1527	332	0.1337	6274	X-RAY DIFFRACTION	99
1.9819-2.0864	0.1567	337	0.1335	6343	X-RAY DIFFRACTION	99
2.0864-2.2171	0.148	318	0.1331	6378	X-RAY DIFFRACTION	100
2.2171-2.3882	0.1538	313	0.1381	6411	X-RAY DIFFRACTION	100
2.3882-2.6285	0.1536	329	0.1421	6397	X-RAY DIFFRACTION	100
2.6285-3.0088	0.1438	341	0.1377	6379	X-RAY DIFFRACTION	100
3.0088-3.7904	0.1505	370	0.1285	6373	X-RAY DIFFRACTION	100
3.7904-41.8461	0.1277	303	0.1288	6470	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.2672	-0.308	-0.1276	1.9603	0.9728	1.1276	0.0146	0.0164	-0.0295	-0.006	-0.0698	0.0491	0.0494	-0.1185	0.0756	0.0626	-0.0159	-0.0026	0.1048	-0.0121	0.0882	-11.425	-16.8561	-29.5721
2	0.3673	-0.0559	0.1102	0.5972	0.0821	0.7169	0.0115	-0.0649	-0.047	0.1165	-0.013	-0.0006	0.1354	-0.0311	0.0092	0.1183	-0.0244	-0.0081	0.0784	0.0123	0.0792	-1.6061	-22.3949	-17.5164
3	0.8372	0.4667	0.5735	0.8302	0.5896	0.5411	-0.0013	-0.0022	0.0195	0.0694	-0.0082	0.022	0.055	-0.05	0.0018	0.0903	-0.0069	0.0019	0.0912	0.0028	0.0688	-1.7405	-5.505	-11.1926
4	0.5873	0.2026	-0.0126	0.7458	0.095	0.7088	0.024	-0.0003	-0.0718	0.0371	0.0014	-0.0673	0.0609	0.0127	-0.0177	0.0525	0.0026	-0.0106	0.0483	-0.0015	0.0544	5.6575	-16.5424	-27.6888
5	1.7762	-0.4942	0.7879	1.5217	-0.321	1.685	0.0366	-0.0735	-0.0239	-0.0191	0.0399	-0.1332	-0.069	0.0684	-0.0645	0.0581	-0.0143	0.018	0.0592	-0.0162	0.0702	13.5706	-4.8734	-33.9671
6	5.1079	-2.9421	1.9395	3.1582	-0.9778	1.9008	0.0849	0.2219	0.0382	-0.1967	-0.0713	-0.2175	-0.0491	0.2443	0.0067	0.0742	-0.0081	0.028	0.0793	-0.016	0.0848	13.8563	-11.7036	-43.4816
7	0.9371	-0.046	-0.1527	1.206	0.3343	1.1431	0.0014	0.032	-0.0135	-0.0999	0.0273	0.0287	-0.0872	-0.0836	-0.025	0.0472	-0.0073	0.0012	0.0442	-0.0077	0.0334	-0.0368	-10.7635	-39.8384
8	0.7433	-0.2165	-0.0935	1.2785	0.5477	1.4788	0.0176	0.0608	-0.0459	-0.0925	-0.0278	-0.0073	-0.011	-0.0334	0.0148	0.0637	-0.0046	0.0008	0.0553	-0.014	0.0601	0.1403	-18.7342	-43.4407
9	0.3947	0.0748	-0.0727	2.3246	1.0366	1.1449	0.0323	0.0377	0.0485	-0.0185	-0.0535	0.0608	-0.0499	-0.0964	0.047	0.0555	0.0129	0.0021	0.089	-0.001	0.0893	-13.9364	17.5596	-5.2524
10	0.3839	0.0574	-0.1403	0.7827	0.1221	0.4367	0.0295	0.0586	0.0506	-0.1103	-0.0096	-0.0131	-0.1069	-0.0124	-0.0226	0.111	0.02	0.0145	0.0782	0.0208	0.0824	-1.5784	22.7698	-14.9966
11	1.1179	-0.5245	-0.3692	0.8953	0.4505	0.3796	0.0246	0.0009	-0.0573	-0.1081	-0.0085	0.0292	-0.0597	-0.0432	-0.0206	0.0976	0.0058	-0.0028	0.0855	0.0056	0.0691	-0.9092	5.6439	-21.6884
12	0.5704	-0.2391	-0.0082	0.6826	0.0254	0.639	0.0285	-0.0022	0.0829	-0.0093	-0.0049	-0.0498	-0.0517	0.0123	-0.017	0.0517	-0.0058	0.0113	0.0496	-0.0014	0.0596	2.777	16.7514	-3.747
13	3.0838	1.3336	-1.3553	1.7576	-0.6535	1.3213	0.0071	0.0442	0.0464	0.0458	0.0275	-0.0868	0.0735	0.0527	-0.0259	0.0633	0.0112	-0.0194	0.0591	-0.0068	0.0528	9.5245	5.2802	3.7237
14	6.6341	3.7691	-1.2183	3.5747	-0.4624	0.8895	0.1115	-0.2643	-0.0736	0.2141	-0.1107	-0.1581	0.0193	0.1649	0.0006	0.0984	-0.0018	-0.0225	0.0893	-0.0086	0.0667	7.2978	12.0579	13.5617
15	0.5993	-0.0073	-0.011	0.9111	0.3444	0.817	0.0162	-0.0534	0.0509	0.0969	-0.0129	0.0067	0.0003	-0.0245	0.0027	0.0631	-0.0014	0.0053	0.0537	-0.009	0.0506	-5.5217	16.3581	9.1196

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 80 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 81 through 123 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 124 through 229 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 230 through 254 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 255 through 272 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 273 through 297 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 298 through 341 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 42 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 43 through 80 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 81 through 123 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 124 through 229 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 230 through 254 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 255 through 272 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 273 through 341 )

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