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

ID or keywords:

Entry

Database: PDB / ID: 4zup

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: 1.421 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	4zup.cif.gz	296.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4zup.ent.gz	238.7 KB	Display	PDB format
PDBx/mmJSON format	4zup.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4zup_validation.pdf.gz	459.2 KB	Display	wwPDB validaton report
Full document	4zup_full_validation.pdf.gz	461.4 KB	Display
Data in XML	4zup_validation.xml.gz	35.4 KB	Display
Data in CIF	4zup_validation.cif.gz	56 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zu/4zup ftp://data.pdbj.org/pub/pdb/validation_reports/zu/4zup	HTTPS FTP

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Related structure data

Related structure data	4zumC 4zunC 4zuoC 4zuqC 4zurC 3q9bS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3q9e-5 3q9f-4 4zum-d 3q9c-5 4zuo-d 3q9c-4 3q9b-1 3q9e-4 6pic-1 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

74 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)	44.715, 120.903, 64.146
Angle α, β, γ (deg.)	90.00, 96.98, 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, 938 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-5XA / 5-amino-N-hydroxypentanamide Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₂N₂O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 920 / 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: 2.37 Å³/Da / Density % sol: 48.01 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M KNO3, 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: Oct 23, 2013
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: 1.42→38.7 Å / Num. obs: 126724 / % possible obs: 100 % / Redundancy: 7.2 % / R_merge(I) obs: 0.07 / Net I/σ(I): 24.3
Reflection shell	Resolution: 1.42→1.47 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.398 / Mean I/σ(I) obs: 5 / % 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: 1.421→38.682 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1524	6355	5.02 %
R_work	0.1305	-	-
obs	0.1315	126680	99.91 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.421→38.682 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5129	0	66	920	6115

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5632
X-RAY DIFFRACTION	f_angle_d	1.347	7687
X-RAY DIFFRACTION	f_dihedral_angle_d	13.037	2016
X-RAY DIFFRACTION	f_chiral_restr	0.09	814
X-RAY DIFFRACTION	f_plane_restr	0.007	1035

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 (%)
1.4207-1.4368	0.1855	221	0.1778	3875	X-RAY DIFFRACTION	98
1.4368-1.4537	0.1663	213	0.1702	3985	X-RAY DIFFRACTION	100
1.4537-1.4715	0.1806	206	0.1599	4046	X-RAY DIFFRACTION	100
1.4715-1.4901	0.179	224	0.1509	4016	X-RAY DIFFRACTION	100
1.4901-1.5097	0.1634	175	0.1415	3966	X-RAY DIFFRACTION	100
1.5097-1.5304	0.1515	220	0.1355	4044	X-RAY DIFFRACTION	100
1.5304-1.5522	0.1539	214	0.1278	3981	X-RAY DIFFRACTION	100
1.5522-1.5754	0.1686	187	0.1281	4036	X-RAY DIFFRACTION	100
1.5754-1.6	0.1359	204	0.1273	4041	X-RAY DIFFRACTION	100
1.6-1.6263	0.1538	213	0.1238	3972	X-RAY DIFFRACTION	100
1.6263-1.6543	0.1383	226	0.1228	4016	X-RAY DIFFRACTION	100
1.6543-1.6844	0.1313	213	0.1249	4001	X-RAY DIFFRACTION	100
1.6844-1.7168	0.155	231	0.1279	3977	X-RAY DIFFRACTION	100
1.7168-1.7518	0.1532	230	0.1315	3999	X-RAY DIFFRACTION	100
1.7518-1.7899	0.1733	222	0.1363	4035	X-RAY DIFFRACTION	100
1.7899-1.8316	0.1707	228	0.1323	3957	X-RAY DIFFRACTION	100
1.8316-1.8774	0.1338	193	0.128	4050	X-RAY DIFFRACTION	100
1.8774-1.9281	0.139	231	0.1288	3974	X-RAY DIFFRACTION	100
1.9281-1.9849	0.1413	234	0.1268	3985	X-RAY DIFFRACTION	100
1.9849-2.0489	0.1543	222	0.1264	4011	X-RAY DIFFRACTION	100
2.0489-2.1221	0.1268	208	0.1275	4034	X-RAY DIFFRACTION	100
2.1221-2.2071	0.1626	218	0.1287	3992	X-RAY DIFFRACTION	100
2.2071-2.3075	0.1631	194	0.1328	4012	X-RAY DIFFRACTION	100
2.3075-2.4292	0.1628	233	0.1363	4006	X-RAY DIFFRACTION	100
2.4292-2.5813	0.1678	197	0.1359	4059	X-RAY DIFFRACTION	100
2.5813-2.7806	0.1538	194	0.1343	4035	X-RAY DIFFRACTION	100
2.7806-3.0603	0.1508	205	0.1348	4043	X-RAY DIFFRACTION	100
3.0603-3.5029	0.1425	223	0.1235	4006	X-RAY DIFFRACTION	100
3.5029-4.4123	0.1512	180	0.1124	4075	X-RAY DIFFRACTION	100
4.4123-38.6961	0.1463	196	0.1349	4096	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	0.4474	0.3799	-0.2581	2.4166	-1.3448	1.5582	-0.0137	-0.017	-0.0013	0.0319	-0.0849	-0.0782	0.0142	0.1019	0.1126	0.0875	0.0146	-0.0045	0.1279	0.0072	0.1176	11.4148	16.3762	29.6594
2	0.3267	-0.0061	0.1253	0.8057	-0.4644	0.8854	0.0057	0.0416	-0.0428	-0.1477	-0.0255	0.0104	0.1526	0.03	0.0311	0.1532	0.0233	-0.0059	0.1089	-0.0128	0.1051	1.2639	10.4367	18.0108
3	1.1943	-0.7746	0.5461	1.1692	-0.6224	0.4097	0.0034	0.0026	0.0443	-0.0826	-0.0199	-0.0578	0.0613	0.0592	0.0111	0.1277	0.0049	0.0059	0.1221	-0.0004	0.1021	1.9147	27.9365	11.139
4	2.8261	1.7619	-1.6898	3.2601	-2.2034	3.0644	-0.0561	0.125	-0.0412	-0.1655	0.1	0.1138	0.288	-0.0699	-0.0029	0.1268	0.0128	-0.0175	0.0864	-0.0126	0.097	0.5437	6.7991	24.0465
5	0.5766	-0.1644	-0.1122	0.9357	-0.1591	0.8047	0.0167	0.0181	-0.0371	-0.021	0.0147	0.102	0.0044	-0.0441	-0.0307	0.072	-0.0042	-0.0059	0.0729	0.0046	0.0756	-8.2957	20.492	29.3587
6	6.3947	4.1029	2.9341	4.0496	2.0432	2.2358	0.0822	-0.2762	0.0421	0.2519	-0.1056	0.242	-0.0097	-0.2484	0.0523	0.1241	0.009	0.0463	0.0997	0.0149	0.111	-13.465	21.4606	43.5084
7	0.7552	-0.1154	0.2955	1.3671	-0.2407	1.2703	-0.0005	-0.0239	-0.0051	0.1072	-0.0013	-0.022	-0.0333	0.0615	-0.0004	0.0963	0.0029	0.0097	0.0851	0.0037	0.0767	-0.6685	17.175	42.0413
8	0.3716	-0.1123	-0.0359	2.6164	-1.192	1.3912	0.0148	-0.0276	0.0009	0.0293	-0.0763	-0.1022	-0.0435	0.1001	0.0809	0.0755	-0.0102	-0.0042	0.1189	0.0008	0.1228	14.0715	51.0549	5.5341
9	0.3505	0.0407	-0.264	0.9988	-0.3388	0.7749	0.0345	-0.0493	0.0482	0.1916	-0.0119	0.0256	-0.1368	0.0118	-0.0205	0.1413	-0.0189	0.0099	0.1037	-0.0195	0.1115	1.5384	56.3468	14.7488
10	1.3503	0.8482	-0.1568	1.0983	-0.3082	0.2964	0.0404	-0.0028	-0.054	0.1532	-0.0145	-0.0467	-0.0466	0.0504	-0.0324	0.1342	-0.0022	-0.0075	0.1104	-0.0068	0.0974	0.7454	38.8402	21.3817
11	2.3598	-0.9488	1.2536	3.2245	-2.1004	3.8624	0.0208	-0.1165	0.1053	0.1434	0.06	0.1028	-0.2545	-0.0923	-0.0419	0.1109	-0.0113	0.0239	0.0829	-0.0197	0.1167	1.9446	60.3328	8.174
12	0.8121	0.1943	0.0039	1.0125	-0.0907	0.8411	0.0255	0.0002	0.0476	0.0054	-0.0189	0.0612	-0.0088	-0.0272	-0.0061	0.0617	0.0051	0.0049	0.0693	-0.0005	0.0671	-3.9817	47.9777	2.6405
13	2.0521	-0.3847	-0.8943	1.334	0.0612	1.1202	0.0087	0.0547	0.0434	-0.1339	0.0143	0.0717	0.0645	-0.0807	-0.0252	0.0935	-0.0088	-0.0341	0.0892	-0.003	0.0793	-8.2409	41.6757	-8.4979
14	0.55	0.1278	-0.0211	1.1649	-0.3265	0.8748	0.0026	0.0334	0.0271	-0.116	-0.0053	-0.0376	0.0003	0.038	0.0031	0.0831	0.005	0.0027	0.0793	0.0038	0.0725	5.4091	49.6295	-9.1159

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 143 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 144 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 341 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 42 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 43 through 80 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 81 through 123 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 124 through 144 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 145 through 229 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 230 through 272 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 273 through 341 )

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