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

ID or keywords:

Entry

Database: PDB / ID: 4zuo

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 / epigenetic regulation of gene expression / metal ion binding
Similarity search - Function

Biological species

Mycoplana ramosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.33 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
Supersession	Aug 5, 2015	ID: 4K6Q
Revision 1.1	Aug 5, 2015	Group: Other
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zuo.cif.gz	304 KB	Display	PDBx/mmCIF format
PDB format	pdb4zuo.ent.gz	244.7 KB	Display	PDB format
PDBx/mmJSON format	4zuo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zuo_validation.pdf.gz	461 KB	Display	wwPDB validaton report
Full document	4zuo_full_validation.pdf.gz	463 KB	Display
Data in XML	4zuo_validation.xml.gz	36.5 KB	Display
Data in CIF	4zuo_validation.cif.gz	58.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zu/4zuo ftp://data.pdbj.org/pub/pdb/validation_reports/zu/4zuo	HTTPS FTP

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Related structure data

Related structure data	4zumC 4zunC 4zupC 4zuqC 4zurC 3q9bS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3q9f-4 4zum-d 3q9c-6 3q9e-4 3q9c-4 3q9e-5 4zup-d 3q9c-5 3q9b-1 6pic-4 3q9f-6 3q9c-1 4zur-d 3q9b-2 6pic-2 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
Related items in Molecule of the Month	#135 - Mar 2011 Integrase similarity (1)

Deposited unit

A: Acetylpolyamine aminohydrolase

B: Acetylpolyamine aminohydrolase

hetero molecules

73.9 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)	44.998, 121.076, 64.417
Angle α, β, γ (deg.)	90.00, 96.75, 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, 1021 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₄N
#5: Chemical	ChemComp-XS6 / 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide Mass: 203.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₂₁N₃O₂
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1008 / 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: 2.4 Å³/Da / Density % sol: 48.66 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M NH4Cl, 20% (w/v) PEG 3,350 Additional 2 day soaking in precipitant solution supplemented with 2.5 mM inhibitor

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.069 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 14, 2015
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.069 Å / Relative weight: 1
Reflection	Resolution: 1.33→38.9 Å / Num. obs: 155090 / % possible obs: 99.3 % / Redundancy: 6.9 % / R_merge(I) obs: 0.054 / Net I/σ(I): 23.4
Reflection shell	Resolution: 1.33→1.38 Å / Redundancy: 6.6 % / R_merge(I) obs: 0.272 / Mean I/σ(I) obs: 6.8 / % possible all: 98.4

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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: 1.33→38.84 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 13.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1474	7777	5.02 %
R_work	0.1329	-	-
obs	0.1336	155046	99.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.33→38.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5128	0	64	1008	6200

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5739
X-RAY DIFFRACTION	f_angle_d	1.338	7826
X-RAY DIFFRACTION	f_dihedral_angle_d	12.664	2065
X-RAY DIFFRACTION	f_chiral_restr	0.086	824
X-RAY DIFFRACTION	f_plane_restr	0.007	1047

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 (%)
1.3305-1.3456	0.1971	252	0.1726	4712	X-RAY DIFFRACTION	96
1.3456-1.3614	0.2016	256	0.161	4840	X-RAY DIFFRACTION	98
1.3614-1.378	0.1807	279	0.1575	4835	X-RAY DIFFRACTION	99
1.378-1.3955	0.1729	267	0.1505	4868	X-RAY DIFFRACTION	99
1.3955-1.4138	0.1796	260	0.1499	4858	X-RAY DIFFRACTION	99
1.4138-1.4332	0.1563	222	0.1467	4918	X-RAY DIFFRACTION	99
1.4332-1.4537	0.1708	262	0.1405	4950	X-RAY DIFFRACTION	99
1.4537-1.4754	0.1555	224	0.1384	4877	X-RAY DIFFRACTION	99
1.4754-1.4984	0.1552	257	0.1375	4949	X-RAY DIFFRACTION	99
1.4984-1.523	0.1536	282	0.1354	4790	X-RAY DIFFRACTION	99
1.523-1.5493	0.1443	247	0.1302	4946	X-RAY DIFFRACTION	99
1.5493-1.5775	0.1474	264	0.1316	4924	X-RAY DIFFRACTION	99
1.5775-1.6078	0.1559	273	0.1273	4921	X-RAY DIFFRACTION	99
1.6078-1.6406	0.1687	265	0.1316	4869	X-RAY DIFFRACTION	100
1.6406-1.6763	0.1416	254	0.1295	4955	X-RAY DIFFRACTION	100
1.6763-1.7153	0.1491	283	0.1263	4877	X-RAY DIFFRACTION	100
1.7153-1.7582	0.1347	270	0.1315	4944	X-RAY DIFFRACTION	100
1.7582-1.8057	0.1547	271	0.1335	4952	X-RAY DIFFRACTION	100
1.8057-1.8588	0.1591	251	0.1341	4919	X-RAY DIFFRACTION	100
1.8588-1.9188	0.1643	256	0.1395	4938	X-RAY DIFFRACTION	100
1.9188-1.9874	0.1525	291	0.1359	4933	X-RAY DIFFRACTION	100
1.9874-2.067	0.1465	247	0.1377	4970	X-RAY DIFFRACTION	100
2.067-2.1611	0.1574	256	0.1351	4959	X-RAY DIFFRACTION	100
2.1611-2.275	0.1491	248	0.1304	4947	X-RAY DIFFRACTION	100
2.275-2.4175	0.157	230	0.1364	4982	X-RAY DIFFRACTION	100
2.4175-2.6041	0.1362	250	0.1384	4967	X-RAY DIFFRACTION	100
2.6041-2.8661	0.1402	279	0.1309	4955	X-RAY DIFFRACTION	100
2.8661-3.2806	0.1381	265	0.1309	4957	X-RAY DIFFRACTION	100
3.2806-4.1325	0.1248	244	0.1189	4795	X-RAY DIFFRACTION	96
4.1325-38.8567	0.1391	272	0.1268	4962	X-RAY DIFFRACTION	99

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	0.7934	-0.1383	-0.2427	3.1723	-1.7009	2.0915	0.0277	-0.074	0.0334	-0.0227	-0.0752	-0.1054	-0.0245	0.1465	0.0692	0.0864	-0.009	-0.0016	0.1381	-0.0054	0.1397	-4.4425	18.2859	-26.2188
2	0.5623	0.0828	-0.3311	1.2335	-0.3246	0.8462	0.0536	-0.0827	0.0773	0.1771	-0.0355	0.0179	-0.1555	0.0403	-0.0141	0.1503	-0.0251	0.0087	0.1179	-0.0305	0.1254	-16.8391	23.9112	-17.3583
3	1.629	0.8827	-0.5753	1.3758	-0.6283	0.4246	0.0425	-0.0581	-0.0544	0.113	-0.0298	-0.0626	-0.0758	0.0996	-0.0217	0.1346	-0.0007	-0.013	0.1278	-0.0092	0.0995	-18.1385	6.5695	-10.2554
4	0.7137	0.2673	0.0108	0.9433	-0.0302	0.762	0.0356	-0.0047	0.1106	0.0065	-0.0168	0.0666	-0.0519	-0.0143	-0.017	0.082	0.0114	0.0085	0.0756	-0.0018	0.0888	-21.6407	17.9509	-28.246
5	2.9618	-0.7373	-1.4384	1.4206	0.4281	1.5302	0.0028	-0.0066	0.0457	-0.0826	0.0187	0.0945	0.1167	-0.0748	-0.0125	0.1101	-0.007	-0.0289	0.0966	0.0052	0.0866	-27.8404	6.1848	-35.9304
6	5.5757	-2.4284	-1.3196	2.4212	0.3168	1.0041	0.0636	0.3175	0.046	-0.1983	-0.061	0.097	0.0422	-0.1999	0.009	0.1646	0.007	-0.0368	0.1372	0.0112	0.1129	-26.1189	13.1752	-45.5323
7	0.8006	0.0658	-0.0276	1.1507	-0.44	1.0946	0.0106	0.0621	0.0716	-0.156	-0.0108	-0.0413	0.0152	0.0579	0.0024	0.1164	0.0112	0.0049	0.0933	0.0086	0.092	-13.1946	17.3753	-41.0937
8	0.4961	0.5675	-0.2414	2.5268	-1.513	1.5524	0.0199	-0.0041	-0.0168	-0.0012	-0.0828	-0.0448	0.0385	0.1257	0.0719	0.0987	0.018	-0.0098	0.142	0.0053	0.1358	-7.703	-16.5669	-1.8391
9	0.4408	-0.0635	0.2087	0.8732	-0.3717	1.0804	0.0539	0.0784	-0.0723	-0.1869	-0.0485	0.0122	0.1893	0.0591	0.0047	0.1624	0.0367	-0.0201	0.1177	-0.0217	0.121	-17.2841	-21.747	-14.0135
10	1.4503	-1.0349	0.9463	1.4541	-0.8957	0.684	0.0416	0.0444	0.0538	-0.1209	-0.0474	-0.0763	0.0728	0.0982	-0.0036	0.1272	0.0103	0.0065	0.1311	-0.0069	0.0981	-16.9244	-4.455	-21.0583
11	0.7311	-0.2857	-0.0008	0.8886	-0.1308	0.7675	0.036	0.0103	-0.1041	-0.0429	-0.0037	0.0847	0.0549	-0.0119	-0.029	0.0832	-0.0012	-0.017	0.0807	-0.0012	0.0917	-24.3682	-15.9394	-4.2054
12	2.3497	0.7736	1.4886	2.0258	0.4563	2.5625	0.0326	0.0886	-0.0189	0.0142	0.0584	0.1613	-0.1145	-0.0643	-0.0758	0.0729	0.0229	0.0198	0.0772	0.0166	0.0976	-32.6474	-4.1079	1.4167
13	5.2735	2.5537	2.3906	2.8345	0.7308	2.2478	0.0668	-0.3151	0.0281	0.1822	-0.0398	0.2406	-0.1016	-0.3236	-0.0167	0.1074	0.0142	0.036	0.1198	0.0227	0.1297	-32.8039	-10.8802	11.5552
14	0.7239	0.0172	-0.0122	1.3373	-0.4901	1.0924	0.0177	-0.0601	-0.0583	0.1205	-0.0125	-0.0181	-0.0338	0.0633	-0.0052	0.0874	0.0016	-0.0034	0.0893	0.007	0.0841	-18.7177	-15.0125	10.1794

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 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 229 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 230 through 254 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 255 through 272 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 273 through 341 )

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