PDB-3zku: Isopenicillin N synthase with substrate analogue AhCV

ID or keywords:

Entry

Database: PDB / ID: 3zku

Title

Isopenicillin N synthase with substrate analogue AhCV

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 / L-ascorbic acid binding / iron ion binding / cytosol
Similarity search - Function

Biological species

Emericella nidulans (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

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

Citation

Journal: Chembiochem / Year: 2013
Title: The Interaction of Isopenicillin N Synthase with Homologated Substrate Analogues Delta-(L-Alpha-Aminoadipoyl)-L-Homocysteinyl-D-Xaa Characterised by Protein Crystallography.
Authors: Daruzzaman, A. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.

History

Deposition	Jan 24, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2013	Group: Database references
Revision 1.2	Apr 10, 2013	Group: Database references / Other
Revision 1.3	Jul 5, 2017	Group: Refinement description / Category: software
Revision 1.4	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 / 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 / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	May 8, 2024	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zku.cif.gz	149.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3zku.ent.gz	119.3 KB	Display	PDB format
PDBx/mmJSON format	3zku.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3zku_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	3zku_full_validation.pdf.gz	1 MB	Display
Data in XML	3zku_validation.xml.gz	18.7 KB	Display
Data in CIF	3zku_validation.cif.gz	26.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zk/3zku ftp://data.pdbj.org/pub/pdb/validation_reports/zk/3zku	HTTPS FTP

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Related structure data

Related structure data	3zkyC 1bk0S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1qjf-d 1bk0-d 6y0p-d 4bb3-d 5zzp-d 1hb1-d 1w06-d 2ivj-d 2vbb-d 1qje-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

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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 software

Unit cell

Length a, b, c (Å)	46.480, 71.105, 101.045
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 / ISOPENICILLIN N SYNTHETASE / IPNS Mass: 37563.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (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-HCV / N-[(5S)-5-amino-5-carboxypentanoyl]-L-homocysteyl-D-valine / Delta-L-alpha-aminoadipoyl-L-homocysteinyl-D-valine Mass: 377.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₇N₃O₆S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.26 Å³/Da / Density % sol: 46 % / Description: NONE
Crystal grow	pH: 8.5 Details: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL PH 8.5, 2.0MM FERROUS SULPHATE, 2.6MG/ML SUBSTRATE, 25MG/ML IPNS

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: MARRESEARCH / Detector: CCD / Date: Apr 27, 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→42 Å / Num. obs: 66426 / % possible obs: 99.4 % / Redundancy: 4.4 % / B_iso Wilson estimate: 12.9 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 22.6
Reflection shell	Resolution: 1.4→1.43 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.25 / Mean I/σ(I) obs: 4.6 / % possible all: 89.1

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
MOSFLM		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK0

1bk0

Resolution: 1.4→41.22 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.96 / SU B: 1.475 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1827	2646	4 %	RANDOM
R_work	0.16125	-	-	-
obs	0.16212	63701	99.31 %	-

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: 15.446 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	0 Å²
2-	-	0.4 Å²	0 Å²
3-	-	-	-0.45 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→41.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2616	0	26	257	2899

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.019	2782
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2553
X-RAY DIFFRACTION	r_angle_refined_deg	2.039	1.944	3794
X-RAY DIFFRACTION	r_angle_other_deg	1.016	3	5887
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.489	5	336
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.263	24.577	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.034	15	432
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.683	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.176	0.2	400
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	3215
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	673
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: 1.4→1.436 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.195	191	-
R_work	0.181	4261	-
obs	-	-	91.6 %

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	21.7277	-11.4682	-15.6656	17.1964	12.959	25.1227	0.1535	0.3801	-0.1469	-0.3287	-0.6269	0.7998	-0.0742	-1.3564	0.4734	0.0397	-0.0012	-0.0629	0.1383	0.0021	0.1408	-8.418	43.09	-7.048
2	0.6918	0.3908	-0.1544	0.5409	-0.4558	1.3104	-0.0626	0.1004	-0.0032	-0.0593	0.0326	-0.001	0.0813	-0.0911	0.03	0.0484	-0.0152	-0.0113	0.0559	0.0093	0.0304	6.051	31.398	-16.827
3	1.1205	0.6112	3.1234	0.7558	1.8156	8.7648	0.0284	-0.1678	-0.0145	0.0356	0.0007	-0.0181	0.0065	-0.4478	-0.0291	0.0651	-0.003	0.0041	0.0733	0.0181	0.0375	5.335	20.725	8.84
4	2.0346	1.1053	-0.0437	1.0547	1.0162	2.6695	0.0103	0.0352	-0.0248	0.0533	0.108	-0.0337	-0.039	0.2295	-0.1184	0.0731	0.0112	0.0125	0.0719	-0.0112	0.037	18.745	32.753	20.322
5	1.2062	-0.2541	-0.3508	0.345	0.1004	0.4278	-0.017	-0.1057	0.0584	0.0192	0.0191	-0.0478	-0.0249	0.0207	-0.0021	0.0392	-0.0001	-0.0171	0.0506	-0.0024	0.0546	19.03	31.501	10.482
6	1.6212	1.2091	-0.5737	1.2494	-0.1154	0.7844	0.0201	-0.1379	0.0106	0.0942	-0.0334	0.0011	0.09	0.082	0.0133	0.0481	0.0116	-0.0056	0.0417	0.013	0.0575	19.604	23.301	10.533
7	0.0663	-0.0994	0.2743	0.6967	-0.9103	1.962	-0.0207	0.0368	-0.0026	-0.0581	0.0021	-0.0231	0.0453	0.0379	0.0187	0.0473	-0.0111	0.0023	0.051	0.0056	0.0447	15.442	29.146	-10.443
8	2.0251	-0.6433	3.7785	0.4071	-1.3609	7.1773	0.0493	0.2082	0.0322	-0.0916	-0.1614	-0.088	0.1686	0.4552	0.1121	0.0546	0.0009	0.0389	0.1053	0.0231	0.0486	22.479	33.88	-16.38
9	3.4538	-1.8164	-0.3155	2.8221	-0.1159	2.4025	0.0166	0.1089	0.1061	-0.0484	-0.037	-0.1704	0.0479	0.1406	0.0204	0.0286	0.0049	0.0089	0.0457	0.0099	0.0632	25.367	28.883	-5.391
10	8.383	-0.6022	-5.3215	0.2597	0.3038	3.413	0.1075	0.0451	0.0728	0.0496	-0.0365	0.0422	-0.0988	-0.037	-0.0711	0.0458	-0.002	0.0023	0.0842	-0.0173	0.0655	6.233	31.965	9.436
11	0.6984	3.1682	-0.9077	14.9813	-3.1604	2.7122	0.1027	0.0056	0.0139	0.4822	-0.092	0.0578	-0.2419	-0.1885	-0.0106	0.0922	0.0142	-0.025	0.0543	-0.0182	0.0586	-3.832	41.517	17.961
12	0.6588	-0.2139	-0.4429	0.6683	0.1461	0.2989	0.0601	-0.0368	0.0721	0.012	-0.018	0.0443	-0.0449	0.0229	-0.0421	0.0411	-0.0044	-0.0011	0.0444	-0.0043	0.0693	4.715	42.931	2.543
13	1.955	0.0203	-0.9371	1.4148	-0.5665	0.6836	-0.0215	0.0915	-0.0395	0.0574	-0.0173	0.0258	-0.0026	-0.0694	0.0388	0.026	-0.0261	0.0009	0.0941	-0.043	0.0642	-2.339	37.649	0.241
14	2.9576	1.3178	0.1633	9.3962	-1.3663	0.3127	0.2148	0.1367	0.2637	-0.3484	-0.3207	0.5344	0.0958	0.0083	0.1059	0.0337	0.0068	0.0207	0.1274	-0.0973	0.2127	-3.83	41.244	-4.749
15	0.6235	-0.0145	-0.4353	0.3145	-0.0118	0.5744	0.0445	0.0262	0.0645	-0.0413	-0.035	0.0345	-0.0666	-0.0243	-0.0095	0.037	-0.004	-0.0064	0.0392	0.007	0.0574	6.972	41.178	-4.418
16	1.2114	0.0543	-1.0181	0.1951	-0.2962	1.4812	-0.0281	0.0336	0.0953	-0.0074	-0.0236	-0.0279	-0.0806	-0.0441	0.0517	0.0537	0.0113	-0.0219	0.0429	0.006	0.068	16.198	34.395	-0.683
17	4.8541	-1.251	8.1587	2.932	-4.1361	15.3691	-0.2017	0.2239	-0.0153	0.1123	0.2216	-0.0282	-0.5049	0.134	-0.0199	0.137	0.036	0.039	0.0726	0.0302	0.0329	19.264	47.97	-19.385
18	3.2045	1.7489	2.653	1.6138	1.4576	2.1968	-0.3597	0.352	0.2013	-0.1333	0.1526	-0.1555	-0.3354	0.2917	0.2071	0.1323	-0.0599	-0.0138	0.0589	0.0556	0.1517	23.743	51.347	-15.482
19	4.5353	-0.5047	-3.7439	4.2324	0.4699	3.3201	0.0517	-0.2682	0.2438	0.2933	-0.0037	-0.1605	-0.097	0.253	-0.048	0.0502	-0.0187	-0.0414	0.0321	0.0043	0.1194	23.14	43.36	0.233
20	28.8122	-21.0584	-11.9577	15.3916	8.7399	4.9632	-0.3121	-0.7362	0.7117	0.2477	0.5691	-0.5143	0.1471	0.3001	-0.257	0.2249	-0.0841	-0.0295	0.1113	-0.0674	0.1406	14.936	47.769	8.068

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 8
2	X-RAY DIFFRACTION	2	A	9 - 49
3	X-RAY DIFFRACTION	3	A	50 - 66
4	X-RAY DIFFRACTION	4	A	67 - 86
5	X-RAY DIFFRACTION	5	A	87 - 119
6	X-RAY DIFFRACTION	6	A	120 - 143
7	X-RAY DIFFRACTION	7	A	144 - 166
8	X-RAY DIFFRACTION	8	A	167 - 174
9	X-RAY DIFFRACTION	9	A	175 - 180
10	X-RAY DIFFRACTION	10	A	181 - 192
11	X-RAY DIFFRACTION	11	A	193 - 201
12	X-RAY DIFFRACTION	12	A	202 - 224
13	X-RAY DIFFRACTION	13	A	225 - 234
14	X-RAY DIFFRACTION	14	A	235 - 246
15	X-RAY DIFFRACTION	15	A	247 - 278
16	X-RAY DIFFRACTION	16	A	279 - 293
17	X-RAY DIFFRACTION	17	A	294 - 302
18	X-RAY DIFFRACTION	18	A	303 - 311
19	X-RAY DIFFRACTION	19	A	312 - 321
20	X-RAY DIFFRACTION	20	A	322 - 327

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