PDB-8bsy: IPNS H270D variant in complex with Fe and ACV after 30s O2 exposure

ID or keywords:

Entry

Database: PDB / ID: 8bsy

Title

IPNS H270D variant in complex with Fe and ACV after 30s O2 exposure

Components

Isopenicillin N synthase

Keywords

OXIDOREDUCTASE / Isopenicillin N synthase / antiobiotic biosynthesis / penicillin / beta lactam / oxygenase / anaerobic

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

Aspergillus nidulans FGSC A4 (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Rabe, P. / Schofield, C.J.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: IPNS H270D variant in complex with Fe and ACV after 30s O2 exposure
Authors: Rabe, P. / Schofield, C.J.

History

Deposition	Nov 26, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 13, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bsy.cif.gz	161.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8bsy.ent.gz	123.1 KB	Display	PDB format
PDBx/mmJSON format	8bsy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8bsy_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8bsy_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8bsy_validation.xml.gz	18.3 KB	Display
Data in CIF	8bsy_validation.cif.gz	28.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bs/8bsy ftp://data.pdbj.org/pub/pdb/validation_reports/bs/8bsy	HTTPS FTP

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Related structure data

Related structure data	6zaeS 7zoe 8a4g 8ali 8alj S: Starting model for refinement
Similar structure data	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

38.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	41.358, 74.432, 101.244
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Isopenicillin N synthase / IPNS Mass: 37540.777 Da / Num. of mol.: 1 / Mutation: H270D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ipnA, ips, AN2622 / Plasmid: pCold_IPNS_H270D / Details (production host): pCold / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ACV / L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE Mass: 363.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₅N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.74 % / Description: needle morphology, 3 um x 3 um x 160 um
Crystal grow	Temperature: 298 K / Method: batch mode / pH: 8.3 / Details: 1.7 M Li2SO4, 0.1 M Tris pH 8.3

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: cryogenic / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 13, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97628 Å / Relative weight: 1
Reflection	Resolution: 1.4→50.62 Å / Num. obs: 62488 / % possible obs: 100 % / Redundancy: 13.3 % / CC_1/2: 0.995 / R_merge(I) obs: 0.178 / R_pim(I) all: 0.05 / R_rim(I) all: 0.185 / Χ²: 0.84 / Net I/σ(I): 7.7 / Num. measured all: 827970
Reflection shell	Resolution: 1.4→1.42 Å / Redundancy: 13.5 % / R_merge(I) obs: 2.066 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3170 / CC_1/2: 0.65 / R_pim(I) all: 0.575 / R_rim(I) all: 2.146 / Χ²: 0.76

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6ZAE

6zae

Resolution: 1.4→41.86 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1961	3101	4.97 %
R_work	0.1685	-	-
obs	0.1698	62341	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.4→41.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2606	0	35	450	3091

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2808
X-RAY DIFFRACTION	f_angle_d	0.969	3842
X-RAY DIFFRACTION	f_dihedral_angle_d	12.355	1022
X-RAY DIFFRACTION	f_chiral_restr	0.089	401
X-RAY DIFFRACTION	f_plane_restr	0.008	515

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 (%)
1.4-1.42	0.309	139	0.2858	2692	X-RAY DIFFRACTION	100
1.42-1.45	0.3218	132	0.2704	2639	X-RAY DIFFRACTION	100
1.45-1.47	0.2926	144	0.2571	2637	X-RAY DIFFRACTION	100
1.47-1.5	0.2616	169	0.2398	2617	X-RAY DIFFRACTION	100
1.5-1.53	0.246	129	0.2212	2696	X-RAY DIFFRACTION	100
1.53-1.56	0.2825	128	0.2128	2642	X-RAY DIFFRACTION	100
1.56-1.59	0.2295	138	0.2035	2689	X-RAY DIFFRACTION	100
1.59-1.63	0.241	132	0.1959	2621	X-RAY DIFFRACTION	100
1.63-1.67	0.2263	137	0.1861	2692	X-RAY DIFFRACTION	100
1.67-1.71	0.2234	142	0.187	2658	X-RAY DIFFRACTION	100
1.71-1.76	0.2163	131	0.1735	2678	X-RAY DIFFRACTION	100
1.76-1.82	0.2296	131	0.1719	2686	X-RAY DIFFRACTION	100
1.82-1.89	0.1803	164	0.1642	2669	X-RAY DIFFRACTION	100
1.89-1.96	0.2251	149	0.1647	2676	X-RAY DIFFRACTION	100
1.96-2.05	0.2113	145	0.1534	2644	X-RAY DIFFRACTION	100
2.05-2.16	0.1688	155	0.1571	2699	X-RAY DIFFRACTION	100
2.16-2.29	0.1816	133	0.1507	2721	X-RAY DIFFRACTION	100
2.29-2.47	0.1855	144	0.1567	2709	X-RAY DIFFRACTION	100
2.47-2.72	0.1844	145	0.1608	2714	X-RAY DIFFRACTION	100
2.72-3.11	0.199	132	0.1614	2746	X-RAY DIFFRACTION	100
3.11-3.92	0.1696	133	0.1467	2800	X-RAY DIFFRACTION	100
3.92-41.86	0.1534	149	0.1521	2915	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	1.5243	0.3624	0.4809	1.9081	1.1141	3.3177	0.0734	-0.0935	-0.0695	0.1012	-0.0693	0.0114	0.1415	-0.1938	0.0193	0.0972	-0.01	0.0104	0.1136	0.0266	0.0884	-15.9185	-4.0586	14.9614
2	1.525	-0.2589	-0.21	0.8918	-0.2469	3.9721	0.0629	-0.0107	-0.0272	-0.0637	0.0326	0.1134	-0.1082	-0.3829	-0.129	0.0894	-0.0197	-0.0126	0.108	-0.0141	0.1308	-22.8021	1.2599	-2.182
3	6.0738	1.0928	-2.323	5.4458	-0.0213	5.3263	0.0772	0.098	0.0725	-0.1043	-0.0859	0.0204	-0.3174	-0.0513	0.0153	0.137	-0.0011	-0.0026	0.0837	-0.0112	0.0515	-10.8855	6.7153	-23.9296
4	0.9003	0.4993	0.3086	1.1095	0.2555	1.8043	-0.0507	0.1095	0.0907	-0.0889	0.0984	-0.0622	-0.2763	0.0783	-0.0376	0.1097	-0.0053	0.0128	0.0905	0.0143	0.0913	-9.2906	10.3077	-13.9079
5	0.6631	-0.4892	0.5971	1.0404	-0.8301	3.5227	0.0079	-0.0371	0.0473	0.0222	0.0186	-0.0035	-0.2472	0.0406	0.0029	0.0978	-0.0142	0.0156	0.0731	-0.0112	0.0947	-10.5612	9.5753	5.8531
6	0.9381	0.0411	0.4728	0.7935	0.1636	1.7831	0.033	0.0029	-0.1042	-0.011	0.0021	0.0188	0.1906	0.0416	-0.0373	0.0826	0.0081	0.0091	0.0774	0.0042	0.093	-12.6894	-8.7148	-4.0098
7	1.4418	-0.3324	0.5907	2.3001	-0.8826	2.9038	0.0432	-0.3711	-0.069	0.2589	-0.1807	-0.2665	0.091	0.7932	0.1449	0.17	-0.0023	-0.0137	0.4015	0.0531	0.1785	5.8685	1.6153	10.4374
8	1.9313	1.1914	1.333	4.078	3.5583	5.9346	-0.0854	0.0743	-0.1206	-0.2115	0.2194	-0.131	0.0898	0.4664	-0.1296	0.1472	0.024	0.0183	0.2055	0.0266	0.171	0.7077	-1.3164	-8.3259

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 64 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 137 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 138 through 182 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 183 through 286 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 287 through 312 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 313 through 331 )

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