PDB-5nnb: Isatin hydrolase A (IHA) from Labrenzia aggregata with isatinate bound

ID or keywords:

Entry

Database: PDB / ID: 5nnb

Title

Isatin hydrolase A (IHA) from Labrenzia aggregata with isatinate bound

Components

isatin hydrolase A

Keywords

HYDROLASE / Isatin / Labrenzia aggregata / isatinate

Function / homology

Function and homology information

arylformamidase activity / L-tryptophan catabolic process to kynurenine / metal ion binding
Similarity search - Function

Biological species

Labrenzia aggregata (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Sommer, T. / Bjerregaard-Andersen, K. / Morth, J.P.

Citation

Journal: Sci Rep / Year: 2018
Title: A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase.
Authors: Sommer, T. / Bjerregaard-Andersen, K. / Uribe, L. / Etzerodt, M. / Diezemann, G. / Gauss, J. / Cascella, M. / Morth, J.P.

History

Deposition	Apr 8, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 16, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 12, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 17, 2024	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	5nnb.cif.gz	406.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5nnb.ent.gz	335.1 KB	Display	PDB format
PDBx/mmJSON format	5nnb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nn/5nnb ftp://data.pdbj.org/pub/pdb/validation_reports/nn/5nnb	HTTPS FTP

-
Related structure data

Related structure data	5nmpC 5nnaC 4m8dS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5kb3-1 5xnk-1 5nmp-2 6nu6-1 5vpu-d 5wxz-1 6nn0-1 6n4n-1 1z5n-d 3nm4-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: isatin hydrolase A

B: isatin hydrolase A

C: isatin hydrolase A

D: isatin hydrolase A

hetero molecules

113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: isatin hydrolase A

B: isatin hydrolase A

hetero molecules

defined by author&software
Evidence: homology, Dimer
56.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: isatin hydrolase A

D: isatin hydrolase A

hetero molecules

defined by author&software
Evidence: gel filtration, Dimer
56.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	38.346, 69.923, 93.536
Angle α, β, γ (deg.)	108.23, 95.26, 103.76
Int Tables number	1
Space group name H-M	P1

#1: Protein	isatin hydrolase A Mass: 27954.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Labrenzia aggregata (bacteria) / Gene: SIAM614_30646 / Production host: Escherichia coli (E. coli) / References: UniProt: A0P0F0
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-92K / Isatinic acid Mass: 165.146 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₇NO₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.04 Å³/Da / Density % sol: 39.57 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15 mg/mL in 5 mM tris-HCl 7.5, 100 mM NaCl 1.0 mM MnCl2, 20 % glycerol and 20 % PEG 1500

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 30, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.8→44.651 Å / Num. obs: 77447 / % possible obs: 93.6 % / Redundancy: 3.4 % / Net I/σ(I): 9.9
Reflection shell	Resolution: 1.8→1.84 Å

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4M8D

4m8d

Resolution: 1.8→19.505 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 29.67

	R_factor	Num. reflection	% reflection
R_free	0.2278	7051	5.04 %
R_work	0.1879	-	-
obs	0.1899	69987	85.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.8→19.505 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7804	0	40	430	8274

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	8096
X-RAY DIFFRACTION	f_angle_d	0.992	11025
X-RAY DIFFRACTION	f_dihedral_angle_d	11.264	2915
X-RAY DIFFRACTION	f_chiral_restr	0.045	1182
X-RAY DIFFRACTION	f_plane_restr	0.005	1466

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 (%)
1.8-1.8204	0.3937	235	0.3347	4486	X-RAY DIFFRACTION	86
1.8204-1.8418	0.3932	238	0.3185	4443	X-RAY DIFFRACTION	86
1.8418-1.8643	0.3851	233	0.3122	4376	X-RAY DIFFRACTION	86
1.8643-1.8879	0.3553	244	0.3126	4490	X-RAY DIFFRACTION	85
1.8879-1.9127	0.3569	231	0.3007	4428	X-RAY DIFFRACTION	85
1.9127-1.9389	0.3547	224	0.2999	4331	X-RAY DIFFRACTION	84
1.9389-1.9665	0.3683	222	0.319	4159	X-RAY DIFFRACTION	81
1.9665-1.9959	0.3361	229	0.3071	4320	X-RAY DIFFRACTION	82
1.9959-2.027	0.3192	246	0.2643	4580	X-RAY DIFFRACTION	88
2.027-2.0602	0.347	234	0.2618	4437	X-RAY DIFFRACTION	87
2.0602-2.0957	0.3092	243	0.2464	4509	X-RAY DIFFRACTION	88
2.0957-2.1338	0.3119	245	0.2554	4576	X-RAY DIFFRACTION	87
2.1338-2.1748	0.3125	224	0.2317	4456	X-RAY DIFFRACTION	87
2.1748-2.2191	0.271	240	0.2348	4441	X-RAY DIFFRACTION	86
2.2191-2.2673	0.2992	235	0.2229	4468	X-RAY DIFFRACTION	86
2.2673-2.3199	0.266	226	0.2263	4316	X-RAY DIFFRACTION	85
2.3199-2.3778	0.265	244	0.209	4528	X-RAY DIFFRACTION	86
2.3778-2.442	0.3081	228	0.2048	4283	X-RAY DIFFRACTION	84
2.442-2.5137	0.241	229	0.2122	4130	X-RAY DIFFRACTION	80
2.5137-2.5947	0.2677	231	0.1993	4327	X-RAY DIFFRACTION	84
2.5947-2.6872	0.2504	234	0.1899	4526	X-RAY DIFFRACTION	87
2.6872-2.7945	0.2156	238	0.1885	4513	X-RAY DIFFRACTION	87
2.7945-2.9213	0.2185	240	0.1782	4521	X-RAY DIFFRACTION	87
2.9213-3.0747	0.2336	239	0.1827	4449	X-RAY DIFFRACTION	87
3.0747-3.2665	0.2247	234	0.1749	4473	X-RAY DIFFRACTION	86
3.2665-3.5174	0.2065	229	0.1704	4338	X-RAY DIFFRACTION	83
3.5174-3.8689	0.1766	229	0.1518	4253	X-RAY DIFFRACTION	83
3.8689-4.423	0.1666	237	0.1369	4526	X-RAY DIFFRACTION	88
4.423-5.5512	0.1424	246	0.1334	4600	X-RAY DIFFRACTION	89
5.5512-19.506	0.1667	244	0.1448	4640	X-RAY DIFFRACTION	90

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	0.7863	-0.3046	-0.754	0.4803	-0.0507	4.2033	0.0804	0.0154	0.225	-0.1396	0.1079	-0.1071	0.0129	0.0332	-0.1836	0.2378	-0.0106	-0.016	0.2613	0.0054	0.319	-14.951	-34.9716	-36.6435
2	1.2421	-0.5639	-1.0318	0.963	0.7853	0.8014	-0.0973	-0.2514	-0.1069	0.1759	0.2085	-0.0419	0.1298	0.1168	-0.1009	0.2699	0.0249	-0.0405	0.3061	0.0153	0.2713	-19.0508	-45.3482	-30.2228
3	0.6928	0.6444	-0.2444	2.8371	-1.6342	2.6326	0.078	-0.0467	0.1785	0.3387	-0.0119	0.008	-0.8245	0.151	-0.036	0.4307	-0.0094	0.0603	0.2919	0.0314	0.3498	-19.8213	-19.7598	-38.1637
4	0.7191	0.527	-0.5216	2.1946	-0.8253	2.0139	0.1693	0.0252	0.176	0.3443	0.0231	0.1103	-0.4631	-0.019	-0.1612	0.3633	0.0176	0.0341	0.29	0.0207	0.3051	-23.6892	-26.6266	-33.3765
5	1.1598	-0.4233	1.1073	4.9756	-2.7707	5.5306	0.1053	0.0566	0.0845	0.0115	-0.0517	0.3063	-0.1941	-0.0946	-0.1636	0.121	0.0281	-0.0098	0.2892	-0.0239	0.2577	-26.4322	-42.4196	-47.7531
6	8.6914	-4.1648	-2.2757	5.3878	1.0572	2.189	0.0051	-0.64	-1.7457	-0.0122	-0.0665	0.2803	0.8199	0.1013	-0.1691	0.5759	0.0957	-0.102	0.4826	0.064	0.5343	-14.2211	-62.6981	-30.0609
7	1.6175	-1.2711	-1.1643	3.559	0.7559	1.8506	-0.0822	-0.2592	0.0336	0.5936	0.1329	0.296	0.2075	-0.0164	0.2749	0.1535	0.0128	-0.0843	0.2527	0.0018	0.2042	-25.474	-43.4841	-23.5365
8	0.9416	-1.715	0.8191	2.8899	-1.3974	0.6011	-0.015	0.0669	0.2335	0.4158	0.0184	-0.5676	-0.2267	0.2237	0.0341	0.1784	0.0222	-0.0531	0.2991	0.0022	0.3188	-3.6236	-50.1044	-40.661
9	0.9026	-0.0139	-0.39	1.1769	0.5011	2.2953	-0.0574	0.1121	-0.0621	-0.3321	0.0523	-0.1038	0.1517	-0.0079	-0.0128	0.2505	0.018	-0.0451	0.3164	-0.0015	0.2831	-17.5662	-57.9184	-55.8734
10	3.0943	1.1357	-2.6282	3.6935	-1.643	5.8663	-0.0163	0.0098	-0.0754	0.0402	0.0099	-0.0785	0.2694	0.0183	0.0038	0.2465	0.0147	-0.0751	0.3174	-0.0199	0.2853	-14.4353	-62.9615	-47.5877
11	0.5555	0.0443	-0.2674	1.3539	0.4879	0.7547	-0.0574	-0.0072	-0.1146	0.1119	0.0634	-0.0626	0.0888	0.0648	-0.0255	0.1701	0.0041	-0.0283	0.2399	0.005	0.2345	-13.938	-52.4629	-45.9881
12	0.888	1.0518	-0.8294	1.673	-1.2616	2.0123	-0.3965	0.1104	-0.3348	-0.6567	0.0885	-0.3647	0.6776	-0.1478	-0.5332	0.3717	-0.0226	0.0637	0.31	-0.0266	0.3613	-15.5539	-63.7764	-1.57
13	0.93	0.5562	0.6884	2.4858	-2.501	2.3731	-0.3927	0.088	-0.4861	-1.4782	0.0768	-0.6997	1.3676	-0.0633	-0.4149	0.829	-0.0747	0.2519	0.3344	-0.047	0.4516	-19.311	-72.5009	0.0071
14	0.7492	0.329	-0.3461	2.0735	-1.8105	3.3831	-0.0567	-0.0807	0.0721	0.0949	0.0679	0.1523	-0.0116	-0.1171	-0.0757	0.2091	-0.0109	-0.0064	0.3018	-0.0244	0.2611	-19.0603	-48.1248	3.9904
15	1.0742	0.6588	-0.4901	1.2298	-0.7651	1.878	-0.0567	0.1736	-0.1508	-0.3015	0.129	0.0141	0.4428	-0.1238	0.0048	0.3773	-0.0579	-0.0109	0.3195	-0.0222	0.2915	-14.9822	-52.6589	-7.2972
16	1.1219	-0.6779	-0.4121	3.6351	0.3494	2.8215	0.1287	-0.116	0.4239	0.1005	-0.0919	0.0465	-0.5944	-0.0964	-0.0448	0.3145	-0.0149	-0.0232	0.3214	-0.0367	0.2379	-11.4789	-36.8721	16.8417
17	1.1404	-1.0587	1.3327	0.9256	-0.5352	5.2766	-0.0717	-0.1415	0.1937	0.0366	0.1149	-0.0805	-0.6977	-0.1699	-0.044	0.3635	0.0105	-0.0095	0.3156	-0.0255	0.2987	-13.0179	-34.2494	7.0185
18	5.384	-2.0101	0.9606	3.7308	0.5433	3.8195	-0.5442	-0.232	1.096	0.251	0.1104	-0.7674	-1.5425	-0.0971	0.1836	0.5606	-0.0399	-0.0805	0.3464	-0.0423	0.3832	-2.9677	-32.067	1.6815
19	1.4064	1.2894	-0.5517	1.3539	-1.3047	3.5141	-0.0486	-0.0496	0.0273	0.0261	0.0054	0.0295	0.0919	-0.1801	0.0395	0.2517	-0.0083	-0.0124	0.2895	-0.0141	0.2609	-13.736	-48.6179	7.6765

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 44 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 95 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 154 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 155 through 256 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 30 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 31 through 44 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 45 through 72 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 73 through 95 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 149 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 150 through 196 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 197 through 256 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 132 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 133 through 256 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 2 through 44 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 45 through 95 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 96 through 139 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 140 through 196 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 197 through 212 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 213 through 256 )

-
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

-
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

-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

-
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