PDB-2vbp: Isopenicillin N synthase with substrate analogue L,L,L-ACAB (unex...

ID or keywords:

Entry

Database: PDB / ID: 2vbp

Title

Isopenicillin N synthase with substrate analogue L,L,L-ACAB (unexposed)

Components

ISOPENICILLIN N SYNTHETASE

Keywords

OXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / PENICILLIN BIOSYNTHESIS / IRON / OXYGENASE / VITAMIN C / METAL-BINDING / MONOCYCLIC INTERMEDIATE / B-LACTAM ANTIBIOTIC

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: 1.5 Å

Authors

Ge, W. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Crystallographic Studies on the Binding of Selectively Deuterated Lld- and Lll-Substrate Epimers by Isopenicillin N Synthase.
Authors: Ge, W. / Clifton, I.J. / Stok, J.E. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.

History

Deposition	Sep 14, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 4, 2008	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 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
Revision 1.4	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

-
Download

PDBx/mmCIF format	2vbp.cif.gz	155.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2vbp.ent.gz	123 KB	Display	PDB format
PDBx/mmJSON format	2vbp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2vbp_validation.pdf.gz	726.7 KB	Display	wwPDB validaton report
Full document	2vbp_full_validation.pdf.gz	728 KB	Display
Data in XML	2vbp_validation.xml.gz	19.3 KB	Display
Data in CIF	2vbp_validation.cif.gz	30.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vb/2vbp ftp://data.pdbj.org/pub/pdb/validation_reports/vb/2vbp	HTTPS FTP

-
Related structure data

Related structure data	2wo7C 1bk0S 1blz 1hb1 1hb2 1hb3 1hb4 1ips 1obn 1oc1 1odm 1odn 1qiq 1qje 1qjf 1uzw 1w03 1w04 1w05 1w06 1w3v 1w3x 2bjs 2bu9 2ivi 2ivj 2jb4 2vau 2vbb 2vbd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2jb4-d 3zky-d 2uw9-d 2ivj-d 6krw-d 5evi-2 2bu9-d 4kba-3 3e8d-1 5a53-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 (3) #111 - Mar 2009 Hydrogenase similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

Deposited unit

A: ISOPENICILLIN N SYNTHETASE

hetero molecules

38.3 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)	40.515, 74.340, 100.704
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 SYNTHETASE / IPNS / ISOPENICILLIN N SYNTHASE 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-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-VB1 / N^6^-[(1R)-2-{[(1S)-1-carboxypropyl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxo-L-lysine Type: L-peptide linking / Mass: 349.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₃H₂₃N₃O₆S
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUES 1-2 NOT SEEN

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.63 % / 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 TRIPEPTIDE, 25MG/ML IPNS

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
Detector	Type: ADSC CCD / Detector: CCD / Date: Feb 23, 2006 / Details: MIRRORS
Radiation	Monochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.488 Å / Relative weight: 1
Reflection	Resolution: 1.4→33.54 Å / Num. obs: 49178 / % possible obs: 81.4 % / Redundancy: 9.9 % / B_iso Wilson estimate: 15.99 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 30.4
Reflection shell	Resolution: 1.4→1.48 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 3.8 / % possible all: 35.4

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK0

1bk0

Resolution: 1.5→59.76 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.959 / SU B: 2.255 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED BY TLSANL FROM REFMAC TLS MODEL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.181	1744	3.9 %	RANDOM
R_work	0.147	-	-	-
obs	0.148	43100	90.5 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 7.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.77 Å²	0 Å²	0 Å²
2-	-	0.04 Å²	0 Å²
3-	-	-	-0.81 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→59.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2645	0	39	443	3127

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	2793
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1865
X-RAY DIFFRACTION	r_angle_refined_deg	1.9	1.952	3812
X-RAY DIFFRACTION	r_angle_other_deg	1.003	3.002	4533
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.405	5	342
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.265	24.792	144
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.857	15	440
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.564	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	397
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3153
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	571
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	591
X-RAY DIFFRACTION	r_nbd_other	0.195	0.2	1981
X-RAY DIFFRACTION	r_nbtor_refined	0.192	0.2	1413
X-RAY DIFFRACTION	r_nbtor_other	0.093	0.2	1448
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	299
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	0.183	0.2	17
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.271	0.2	78
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.19	0.2	61
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	1.276	1.5	2128
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.564	2	2710
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.789	3	1335
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.754	4.5	1095
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: 1.5→1.54 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.416	89
R_work	0.289	2292

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	1.1961	0.6612	-0.4935	5.1022	-2.3017	2.745	-0.0257	0.005	-0.1934	-0.0887	0.0021	-0.0845	0.2278	0.0655	0.0236	0.0373	0.0167	0.0064	0.027	-0.0182	0.0787	18.59	-6.66	-10.324
2	1.0566	0.5523	0.1467	2.5824	0.3677	2.0153	0.0582	0.1174	0.0721	-0.1036	-0.0315	0.0109	-0.0726	0.1562	-0.0267	0.0231	0.0094	0.0005	0.0187	-0.0129	0.0517	14.247	-0.227	-19.65
3	2.2333	1.548	0.6128	2.9442	0.2528	1.3928	-0.0289	0.0723	-0.0893	-0.1828	0.0127	-0.0658	0.0829	0.0461	0.0162	0.0469	0.017	0.0097	0.0218	-0.0081	0.0802	17.476	-3.677	-7.804
4	1.7603	-0.6002	-3.7123	0.9122	1.1336	8.9049	0.0861	-0.1775	0.0899	0.0481	0.0879	-0.1199	0.0627	0.3572	-0.174	0.0117	-0.0203	-0.0141	0.0189	-0.0041	0.0631	24.074	5.428	14.311
5	2.9063	-0.8656	-1.1208	3.1922	-0.2903	3.7213	0.0766	0.0293	0.0865	0.0699	-0.0202	0.0807	-0.1898	-0.2319	-0.0564	0.06	0.0216	0.0071	0.0021	0.0076	0.0338	6.799	7.393	22.929
6	0.38	-0.4206	0.281	0.8672	-0.3075	0.7381	-0.0537	-0.0464	-0.0116	0.114	0.0379	0.0174	-0.0241	-0.0551	0.0158	0.0324	0.0072	0.006	-0.0037	0.0012	0.0585	10.651	4.969	14.73
7	1.8662	-0.2308	-0.2599	0.7184	0.2634	0.614	-0.0167	-0.1406	0.0326	0.072	0.0274	0.0075	-0.069	-0.0005	-0.0107	0.0678	0.002	0.0006	0.0188	-0.0057	0.0765	6.751	16.508	12.159
8	0.5386	0.2617	0.5022	0.4479	0.474	1.8979	0.001	0.0519	0.0165	-0.0263	-0.0104	-0.0115	-0.0826	0.0418	0.0095	0.0292	0.0061	0.0015	0.0034	0.0013	0.0688	13.242	8.771	-4.39
9	0.9153	-0.6944	0.427	1.3886	-0.7885	1.4001	0.0211	0.0523	-0.0665	0.0109	-0.0243	0.0576	-0.0355	0.0309	0.0032	0.0409	-0.0059	0.0001	0.011	-0.0094	0.0834	10.817	5.682	3.699
10	4.142	2.691	1.9334	2.356	1.5324	4.0676	0.1943	-0.2374	-0.1668	0.2153	-0.1317	-0.0192	0.4557	-0.1483	-0.0626	0.0742	-0.006	-0.0129	-0.0211	0.0206	0.0669	14.017	-17.624	16.781
11	0.5437	-0.1268	0.0419	0.5814	-0.1449	0.6911	0.0148	-0.0028	-0.0678	0.0213	-0.0136	-0.0404	0.055	0.0298	-0.0012	0.0129	0.0028	-0.0057	-0.0129	-0.0091	0.0626	12.089	-8.406	0.47
12	6.0027	-1.5048	-2.269	1.4763	0.4713	9.8782	0	-0.0633	-0.1413	-0.089	-0.0012	0.1093	0.2559	-0.3722	0.0012	0.0264	-0.0122	-0.0134	0.0108	-0.0287	0.062	-0.811	-5.75	-10.817
13	0.3836	-0.1387	0.0706	0.5148	-0.0035	0.6007	0.0322	0.0283	-0.0358	-0.0387	-0.0461	0.0214	0.0445	-0.0397	0.0139	0.0391	0.001	-0.0039	0.0166	-0.0085	0.0735	8.043	-2.77	1.153
14	3.2284	-3.9312	-5.2838	5.493	7.0088	16.8281	0.2062	0.562	-0.1968	-0.1364	-0.6503	0.3448	0.4877	-1.8775	0.4442	-0.0486	-0.0495	-0.0361	0.1793	-0.1051	-0.003	-8.755	-3.485	-15.879
15	0.9094	-1.2638	0.8247	1.77	-1.0288	1.7463	-0.0328	-0.1249	-0.1328	0.1931	0.0472	0.0785	0.0725	-0.1634	-0.0144	0.0177	-0.0177	0.0104	-0.0003	-0.0052	0.0729	-1.377	-0.488	7.366

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 19
2	X-RAY DIFFRACTION	2	A	20 - 36
3	X-RAY DIFFRACTION	3	A	37 - 50
4	X-RAY DIFFRACTION	4	A	51 - 69
5	X-RAY DIFFRACTION	5	A	70 - 85
6	X-RAY DIFFRACTION	6	A	86 - 112
7	X-RAY DIFFRACTION	7	A	113 - 134
8	X-RAY DIFFRACTION	8	A	135 - 171
9	X-RAY DIFFRACTION	9	A	172 - 191
10	X-RAY DIFFRACTION	10	A	192 - 208
11	X-RAY DIFFRACTION	11	A	209 - 258
12	X-RAY DIFFRACTION	12	A	259 - 266
13	X-RAY DIFFRACTION	13	A	267 - 299
14	X-RAY DIFFRACTION	14	A	300 - 310
15	X-RAY DIFFRACTION	15	A	311 - 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