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

ID or keywords:

Entry

Database: PDB / ID: 4zum

Title

Crystal structure of acetylpolyamine amidohydrolase from Mycoplana ramosa in complex with a trifluoromethylketone 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: 1.42 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

-
Download

PDBx/mmCIF format	4zum.cif.gz	302.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4zum.ent.gz	243.6 KB	Display	PDB format
PDBx/mmJSON format	4zum.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4zum_validation.pdf.gz	850.7 KB	Display	wwPDB validaton report
Full document	4zum_full_validation.pdf.gz	852.8 KB	Display
Data in XML	4zum_validation.xml.gz	35.2 KB	Display
Data in CIF	4zum_validation.cif.gz	56.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zu/4zum ftp://data.pdbj.org/pub/pdb/validation_reports/zu/4zum	HTTPS FTP

-
Related structure data

Related structure data	4zunC 4zuoC 4zupC 4zuqC 4zurC 3q9bS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4zuo-d 4zup-d 6pic-1 3q9f-4 3q9e-5 6pic-4 3q9c-1 6pht-2 3q9c-6 3q9f-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

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)	45.119, 121.351, 64.295
Angle α, β, γ (deg.)	90.00, 96.76, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
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 / Strain (production host): BL21 (DE3) / References: UniProt: Q48935

-
Non-polymers , 7 types, 947 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-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-FKS / 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol Mass: 258.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₁F₃N₂O₂
#6: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO₃
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 933 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.81 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M LiNO3, 20% (w/v) PEG 3,350

-
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→38.9 Å / Num. obs: 128460 / % possible obs: 99.9 % / Redundancy: 5 % / R_merge(I) obs: 0.07 / Net I/σ(I): 20.4
Reflection shell	Resolution: 1.42→1.47 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.328 / Mean I/σ(I) obs: 4.8 / % possible all: 99.7

-
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: 1.42→38.893 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1531	6458	5.03 %
R_work	0.1329	-	-
obs	0.1339	128411	99.63 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.42→38.893 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5132	0	68	933	6133

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5792
X-RAY DIFFRACTION	f_angle_d	1.341	7922
X-RAY DIFFRACTION	f_dihedral_angle_d	13.406	2089
X-RAY DIFFRACTION	f_chiral_restr	0.088	831
X-RAY DIFFRACTION	f_plane_restr	0.007	1072

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 (%)
1.4204-1.4365	0.2187	179	0.1822	3776	X-RAY DIFFRACTION	93
1.4365-1.4534	0.1882	212	0.1677	4151	X-RAY DIFFRACTION	100
1.4534-1.4712	0.1825	194	0.1648	4012	X-RAY DIFFRACTION	100
1.4712-1.4898	0.1954	225	0.1571	4055	X-RAY DIFFRACTION	100
1.4898-1.5094	0.1763	210	0.1433	4081	X-RAY DIFFRACTION	100
1.5094-1.5301	0.1635	233	0.1328	4010	X-RAY DIFFRACTION	100
1.5301-1.5519	0.1408	210	0.1287	4080	X-RAY DIFFRACTION	100
1.5519-1.5751	0.1617	219	0.1296	4064	X-RAY DIFFRACTION	100
1.5751-1.5997	0.1541	224	0.1254	4080	X-RAY DIFFRACTION	100
1.5997-1.6259	0.1393	211	0.1286	4017	X-RAY DIFFRACTION	100
1.6259-1.654	0.1543	222	0.1227	4105	X-RAY DIFFRACTION	100
1.654-1.684	0.154	227	0.1243	4073	X-RAY DIFFRACTION	100
1.684-1.7164	0.1547	239	0.1224	4004	X-RAY DIFFRACTION	100
1.7164-1.7515	0.1404	198	0.1333	4104	X-RAY DIFFRACTION	100
1.7515-1.7896	0.1464	223	0.1321	4060	X-RAY DIFFRACTION	100
1.7896-1.8312	0.1611	212	0.1327	4046	X-RAY DIFFRACTION	100
1.8312-1.877	0.1483	211	0.1299	4115	X-RAY DIFFRACTION	100
1.877-1.9277	0.1424	217	0.1332	4034	X-RAY DIFFRACTION	100
1.9277-1.9845	0.161	199	0.1349	4102	X-RAY DIFFRACTION	100
1.9845-2.0485	0.1403	221	0.1355	4104	X-RAY DIFFRACTION	100
2.0485-2.1217	0.1726	223	0.1341	4045	X-RAY DIFFRACTION	100
2.1217-2.2067	0.1586	217	0.1295	4037	X-RAY DIFFRACTION	100
2.2067-2.3071	0.1464	227	0.1317	4091	X-RAY DIFFRACTION	100
2.3071-2.4287	0.1618	220	0.1386	4061	X-RAY DIFFRACTION	100
2.4287-2.5808	0.1775	209	0.138	4104	X-RAY DIFFRACTION	100
2.5808-2.78	0.1563	237	0.1328	4057	X-RAY DIFFRACTION	100
2.78-3.0597	0.1478	216	0.1354	4109	X-RAY DIFFRACTION	100
3.0597-3.5022	0.1386	207	0.1284	4106	X-RAY DIFFRACTION	100
3.5022-4.4114	0.1398	213	0.1196	4108	X-RAY DIFFRACTION	100
4.4114-38.9071	0.1347	203	0.1324	4162	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	0.3897	-0.0576	-0.1099	2.9903	-1.374	1.51	0.0258	-0.046	0.0212	0.0225	-0.102	-0.1602	-0.0504	0.1441	0.0869	0.0443	-0.0144	-0.0022	0.1	0.0066	0.0887	-4.3662	17.208	-26.1737
2	0.3926	0.1291	-0.365	1.1264	-0.4922	0.9814	0.049	-0.0386	0.0483	0.1935	-0.0365	0.0259	-0.1653	0.036	-0.0116	0.1093	-0.0206	0.0068	0.0714	-0.0175	0.0829	-17.1743	23.6224	-17.6133
3	1.7109	0.9315	-0.1938	1.2936	-0.3748	0.5883	0.0544	-0.0595	-0.0316	0.1315	-0.0307	-0.0477	-0.0624	0.0741	-0.0303	0.0944	-0.0013	-0.0069	0.0743	-0.0041	0.0623	-18.1645	5.4266	-9.97
4	0.5669	0.1369	0.0097	0.719	-0.0953	0.7999	0.0324	0.0034	0.074	0.0135	-0.0147	0.0579	-0.0476	-0.018	-0.0046	0.0454	0.0086	0.0098	0.0442	0.0021	0.0535	-21.6456	16.6746	-28.3594
5	3.7087	-0.9456	-1.943	1.8041	0.5802	2.1113	0.0211	-0.0073	0.033	-0.0789	0.0156	0.0834	0.0917	-0.074	-0.0312	0.0626	-0.0101	-0.0298	0.0533	0.0064	0.0493	-27.8252	5.0131	-36.0054
6	5.6757	-2.6641	-1.0877	2.3363	0.1069	1.0205	0.0909	0.3142	0.0089	-0.21	-0.078	0.1165	0.038	-0.1892	-0.0027	0.1113	0.001	-0.0317	0.0887	0.0069	0.0704	-26.1478	11.9284	-45.4884
7	0.9232	0.0988	-0.1514	1.1132	-0.3154	1.1893	0.0095	0.044	0.0245	-0.1286	-0.0146	-0.0416	0.0229	0.057	0.0105	0.068	0.0045	0.0062	0.0542	0.0068	0.0474	-13.2606	16.2395	-41.0309
8	0.2708	0.4633	-0.3316	2.7021	-1.5794	1.415	0.0124	-0.0076	-0.0115	-0.0187	-0.0915	-0.0759	0.0421	0.1412	0.0946	0.0527	0.016	-0.0076	0.1055	0.013	0.086	-7.7041	-17.6151	-1.9167
9	0.293	-0.0208	0.1788	1.2427	-0.6542	1.3017	0.0191	0.0351	-0.0441	-0.2167	-0.0418	0.0049	0.1807	0.0474	0.027	0.1228	0.0273	-0.0098	0.0775	-0.0116	0.0775	-17.5339	-23.3893	-13.5565
10	1.405	-1.0335	0.5478	1.4782	-0.625	0.3993	0.0509	0.0537	0.0524	-0.1313	-0.059	-0.0731	0.0758	0.0851	-0.0009	0.0952	0.0063	0.0071	0.0885	0.0019	0.0644	-16.8037	-5.562	-21.2377
11	0.5841	-0.1219	-0.0469	0.7297	-0.1195	0.7586	0.0257	0.0082	-0.0585	-0.0603	-0.0047	0.0677	0.0629	-0.017	-0.0104	0.0542	-0.0034	-0.017	0.0495	0.0026	0.0529	-24.489	-16.8259	-4.2803
12	2.5393	0.7366	1.6793	1.7591	0.5175	3.0297	0.0272	0.0743	-0.0131	0.0282	0.0634	0.1367	-0.113	-0.0413	-0.0652	0.0454	0.0199	0.0193	0.051	0.0176	0.0693	-31.4748	-4.6894	2.2852
13	5.6425	3.1473	2.0059	3.1481	1.0873	1.9061	0.0857	-0.2227	0.065	0.1782	-0.0573	0.2256	-0.0565	-0.2781	-0.0079	0.0777	0.0096	0.0304	0.0856	0.0207	0.0912	-32.8916	-12.139	11.4737
14	0.5894	-0.0091	-0.0539	1.2094	-0.5063	1.126	0.022	-0.0546	-0.0318	0.106	-0.0347	-0.0194	-0.0318	0.0593	0.0109	0.0537	-0.002	-0.0034	0.0572	0.007	0.0478	-18.9351	-16.2742	10.2447

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 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 7 types, 947 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 7 types, 947 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 7 types, 947 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi