PDB-4bb3: Isopenicillin N synthase with the dipeptide substrate analogue AhC

ID or keywords:

Entry

Database: PDB / ID: 4bb3

Title

Isopenicillin N synthase with the dipeptide substrate analogue AhC

Components

ISOPENICILLIN N SYNTHASE

Keywords

OXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS

Function / homology

Function and homology information

isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / iron ion binding / cytosol
Similarity search - Function

Biological species

ASPERGILLUS NIDULANS FGSC A4 (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Daruzzaman, A. / Clifton, I.J. / Rutledge, P.J.

Citation

Journal: Arch.Biochem.Biophys. / Year: 2013
Title: The Crystal Structure of Isopenicillin N Synthase with a Dipeptide Substrate Analogue.
Authors: Daruzzaman, A. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.

History

Deposition	Sep 19, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 17, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 5, 2017	Group: Refinement description / Category: software
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4bb3.cif.gz	156.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4bb3.ent.gz	124.3 KB	Display	PDB format
PDBx/mmJSON format	4bb3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bb/4bb3 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/4bb3	HTTPS FTP

-
Related structure data

Related structure data	1bk0S S: Starting model for refinement
Similar structure data	6y0p-d 2y60-d 2vbb-d 1w05-d 1qjf-d 1hb1-d 2ivj-d 1w03-d 2bjs-d 1odn-d 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
Related items in Molecule of the Month	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (2)

Deposited unit

A: ISOPENICILLIN N SYNTHASE

hetero molecules

38 kDa, 1 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)	46.508, 71.202, 100.884
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	ISOPENICILLIN N SYNTHASE / IPNS Mass: 37563.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS NIDULANS FGSC A4 (mold) / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-KKA / (2S)-2-azanyl-6-oxidanylidene-6-[[(2S)-1-oxidanyl-1-oxidanylidene-4-sulfanyl-butan-2-yl]amino]hexanoic acid Mass: 278.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₈N₂O₅S
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.24 Å³/Da / Density % sol: 45.14 % / Description: NONE
Crystal grow	pH: 8.5 / Details: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL (PH8.5)

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2002 / Details: MIRROR
Radiation	Monochromator: DIAMOND (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 1.4→50.44 Å / Num. obs: 66412 / % possible obs: 99.2 % / Redundancy: 4.4 % / R_merge(I) obs: 0.06 / Net I/σ(I): 14.7
Reflection shell	Resolution: 1.4→1.47 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 3.3 / % possible all: 95.1

-
Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK0

1bk0

Resolution: 1.4→58.28 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.96 / SU B: 1.673 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18836	2647	4 %	RANDOM
R_work	0.17199	-	-	-
obs	0.17265	63693	99.02 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 16.414 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	0 Å²
2-	-	0.23 Å²	0 Å²
3-	-	-	-0.29 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→58.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2645	0	24	278	2947

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.02	2876
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.133	1.945	3947
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.525	5	370
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.353	24.904	157
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.853	15	460
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.867	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.138	0.2	414
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.021	2315
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.398→1.435 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.252	185	-
R_work	0.252	3988	-
obs	-	-	90.05 %

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	20.2892	-24.4207	-12.15	46.2657	28.6051	18.8754	-0.0585	0.6007	-0.1483	0.1336	-1.3044	1.7305	0.0776	-0.9079	1.3629	0.0545	0.0224	-0.0217	0.325	0.0195	0.1881	-6.048	39.877	-8.936
2	1.0562	0.4566	-0.3651	1.0722	-0.5677	1.9433	-0.0785	0.1288	-0.0216	-0.134	0.0283	-0.0529	0.1302	-0.0588	0.0502	0.0847	-0.0168	-0.0108	0.0857	0.0044	0.0466	6.708	31.177	-17.193
3	0.9557	0.7967	2.9966	1.6138	2.8009	9.5465	0.0549	-0.1536	-0.0386	0.1091	0.0502	0.0168	0.1314	-0.4034	-0.1051	0.0733	-0.0172	0.01	0.0817	0.0213	0.0387	6.479	21.378	11.107
4	3.2962	0.6789	-0.0062	2.3651	0.8136	4.1373	0.0085	0.0347	0.0943	0.015	0.0996	-0.1158	-0.1687	0.4143	-0.1081	0.0621	0.0009	-0.0031	0.1007	-0.0146	0.0235	19.917	34.169	19.677
5	1.7354	-0.3411	-0.3768	0.9854	0.126	0.8948	-0.0223	-0.1695	0.0878	0.0572	0.0194	-0.0153	-0.0475	0.0215	0.0029	0.0743	0.0008	-0.0205	0.0758	-0.0056	0.061	17.466	31.671	10.726
6	2.2588	1.1139	-0.4534	2.2383	-0.0748	0.7809	0.0469	-0.2244	0.0252	0.1782	-0.0443	-0.044	0.0019	0.0815	-0.0026	0.0557	0.0058	-0.0203	0.0774	-0.0023	0.0467	24.526	27.229	10.929
7	0.3884	-0.1417	0.2492	1.1824	-1.1243	2.5996	-0.0326	0.0264	-0.0335	-0.0486	0.0005	-0.0159	0.1207	0.0076	0.0321	0.0612	-0.0051	0.0033	0.0567	0.0023	0.0527	15.283	25.986	-4.996
8	2.8408	-0.6954	3.9708	3.1333	-2.3732	7.4693	0.131	0.2996	-0.06	-0.2034	-0.1224	-0.0002	0.2491	0.4666	-0.0087	0.0665	-0.0064	0.0227	0.099	0.0172	0.0435	22.503	33.96	-16.432
9	5.5901	-0.914	-0.8736	4.2722	-0.6204	4.1106	0.0133	0.1279	0.216	-0.0984	-0.0669	-0.2877	0.1232	0.3154	0.0535	0.0448	0.0082	0.0042	0.0633	0.0102	0.0575	25.728	28.695	-5.873
10	6.4095	-0.2136	-3.9844	0.4985	-0.036	2.7277	0.0325	-0.0722	0.054	0.0533	-0.0195	0.0653	-0.0294	-0.0732	-0.0129	0.0487	-0.0075	-0.009	0.0892	-0.0201	0.057	7.416	31.913	8.623
11	11.0681	4.5667	2.4768	22.8582	2.1536	0.6299	0.0995	-0.5342	0.2634	1.8887	-0.2578	0.1677	0.0416	-0.1805	0.1583	0.529	0.2697	-0.2496	0.2462	-0.2203	0.2122	-5.193	40.027	19.664
12	1.4982	-0.7626	1.8648	7.6745	-4.1362	7.525	0.0898	0.0465	0.0365	0.3123	-0.0218	0.0492	-0.0967	0.0758	-0.068	0.0735	0.0079	0.0324	0.0411	-0.03	0.1039	-3.584	48.386	9.84
13	1.3498	-0.1791	-0.6498	0.8419	0.4415	0.5511	0.0682	-0.1383	0.1578	0.0771	0.0083	0.0105	-0.0277	0.0137	-0.0765	0.0633	-0.0038	0.0008	0.0648	-0.0028	0.0587	8.322	41.926	0.654
14	24.8224	-5.7073	-11.2488	3.6165	-0.2461	8.5798	-0.0136	-0.1295	-0.3385	-0.0094	-0.0069	0.1909	0.0212	0.1035	0.0204	0.0358	-0.0487	-0.0042	0.096	-0.0397	0.0837	-1.091	29.418	1.321
15	5.2088	2.4253	0.7237	4.742	0.7903	2.7731	0.0173	0.1761	0.3338	-0.2335	-0.068	0.3181	-0.0258	-0.082	0.0507	0.0335	0.0149	-0.0079	0.0873	0.0006	0.0785	-3.391	42.092	-3.496
16	1.8615	0.5124	-0.4942	1.6464	-0.2214	1.2532	0.0171	0.0829	0.1244	-0.0928	0.0031	0.0266	-0.0643	-0.0237	-0.0202	0.0809	0.0046	-0.0066	0.0741	0.015	0.0559	11.147	40.84	-9.782
17	0.6613	-0.1331	-0.403	0.5257	-0.1095	0.3316	0.0307	-0.0367	0.0109	0.0414	-0.0217	0.0568	-0.0341	0.0055	-0.009	0.0508	-0.0119	-0.0024	0.0904	-0.02	0.0675	4.975	36.838	2.965
18	3.9755	-3.0892	5.7794	4.1986	-6.6539	12.3662	-0.019	0.12	0.1215	0.0083	-0.022	-0.1268	-0.421	0.047	0.0411	0.1229	0.0023	0.0386	0.0318	0.0301	0.0597	22.699	45.087	-14.095
19	3.5633	2.8522	1.568	2.2998	1.6071	9.912	-0.3942	0.3711	-0.0001	-0.3201	0.3087	-0.012	-0.5375	0.7909	0.0856	0.1552	-0.0544	0.0109	0.1181	0.0564	0.1041	22.406	52.444	-18.559
20	4.7639	-0.8603	-3.4861	1.2122	-0.212	4.6365	0.0719	-0.4177	0.3094	0.298	0.0617	-0.0156	-0.245	0.171	-0.1336	0.1237	-0.0393	0.012	0.0713	-0.0277	0.0887	19.162	44.984	3.591

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 11
2	X-RAY DIFFRACTION	2	A	12 - 49
3	X-RAY DIFFRACTION	3	A	50 - 69
4	X-RAY DIFFRACTION	4	A	70 - 86
5	X-RAY DIFFRACTION	5	A	87 - 116
6	X-RAY DIFFRACTION	6	A	117 - 134
7	X-RAY DIFFRACTION	7	A	135 - 166
8	X-RAY DIFFRACTION	8	A	167 - 174
9	X-RAY DIFFRACTION	9	A	175 - 179
10	X-RAY DIFFRACTION	10	A	180 - 192
11	X-RAY DIFFRACTION	11	A	193 - 198
12	X-RAY DIFFRACTION	12	A	199 - 208
13	X-RAY DIFFRACTION	13	A	209 - 223
14	X-RAY DIFFRACTION	14	A	224 - 228
15	X-RAY DIFFRACTION	15	A	229 - 245
16	X-RAY DIFFRACTION	16	A	246 - 266
17	X-RAY DIFFRACTION	17	A	267 - 289
18	X-RAY DIFFRACTION	18	A	290 - 301
19	X-RAY DIFFRACTION	19	A	302 - 309
20	X-RAY DIFFRACTION	20	A	310 - 331

-
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