PDB-9ebm: Piperazate synthase (PipS) in complex with haem and N5-OH-L-ornithine

ID or keywords:

Entry

Database: PDB / ID: 9ebm

Title

Piperazate synthase (PipS) in complex with haem and N5-OH-L-ornithine

Components

Piperazate synthase

Keywords

BIOSYNTHETIC PROTEIN / N-N bond / natural product biosynthesis / heme / piperazate / piperazic acid

Function / homology

PROTOPORPHYRIN IX CONTAINING FE / N~5~-hydroxy-L-ornithine

Function and homology information

Biological species

Streptomyces griseus subsp. griseus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.92 Å

Authors

Higgins, M.A. / Ryan, K.S.

Funding support

Canada, 1items

Citation

Journal: Nat Catal / Year: 2025
Title: Structure and mechanism of haem-dependent nitrogen-nitrogen bond formation in piperazate synthase
Authors: Higgins, M.A. / Shi, X. / Soler, J. / Harland, J.B. / Parkkila, T. / Lehnert, N. / Garcia-Borras, M. / Du, Y.L. / Ryan, K.S.

History

Deposition	Nov 12, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2025	Group: 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.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9ebm.cif.gz	228.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9ebm.ent.gz	152.4 KB	Display	PDB format
PDBx/mmJSON format	9ebm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9ebm_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	9ebm_full_validation.pdf.gz	1.7 MB	Display
Data in XML	9ebm_validation.xml.gz	24.5 KB	Display
Data in CIF	9ebm_validation.cif.gz	32.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eb/9ebm ftp://data.pdbj.org/pub/pdb/validation_reports/eb/9ebm	HTTPS FTP

-
Related structure data

Related structure data	9ebkC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: Piperazate synthase

A: Piperazate synthase

hetero molecules

52 kDa, 2 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)	67.002, 67.002, 479.001
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22
Space group name Hall	P6₁2(x,y,z+5/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: x-y,-y,-z #7: -x,-x+y,-z+2/3 #8: -x,-y,z+1/2 #9: y,x,-z+1/3 #10: -y,-x,-z+5/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/6

Components on special symmetry positions

ID	Model	Components
1	1	B-668- HOH

#1: Protein	Piperazate synthase Mass: 25152.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus subsp. griseus (bacteria) Strain: NRRL F-5144 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ONH / N~5~-hydroxy-L-ornithine Type: L-peptide linking / Mass: 148.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₂N₂O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.09 Å³/Da / Density % sol: 60.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.76 M sodium citrate tribasic dihydrate, 0.1 M sodium cacodylate, pH 6.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97936 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97936 Å / Relative weight: 1
Reflection	Resolution: 1.92→79.83 Å / Num. obs: 50850 / % possible obs: 100 % / Redundancy: 27.3 % / B_iso Wilson estimate: 30.8 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.045 / Net I/σ(I): 13.3
Reflection shell	Resolution: 1.92→1.97 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3343 / CC_1/2: 0.778 / R_pim(I) all: 0.506

-
Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.92→79.83 Å / SU ML: 0.2105 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3401 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2116	2484	4.91 %
R_work	0.174	48148	-
obs	0.1758	50632	99.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 41.67 Å²

Refinement step

Cycle: LAST / Resolution: 1.92→79.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3326	0	118	248	3692

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0073	3562
X-RAY DIFFRACTION	f_angle_d	0.8933	4879
X-RAY DIFFRACTION	f_chiral_restr	0.051	507
X-RAY DIFFRACTION	f_plane_restr	0.0053	633
X-RAY DIFFRACTION	f_dihedral_angle_d	15.7981	2436

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 (%)
1.92-1.96	0.292	134	0.2891	2596	X-RAY DIFFRACTION	100
1.96-2	0.2918	127	0.2726	2609	X-RAY DIFFRACTION	100
2-2.04	0.2829	138	0.249	2597	X-RAY DIFFRACTION	99.96
2.04-2.09	0.2801	142	0.2386	2615	X-RAY DIFFRACTION	100
2.09-2.14	0.2789	143	0.2301	2579	X-RAY DIFFRACTION	99.93
2.14-2.2	0.2834	122	0.2145	2614	X-RAY DIFFRACTION	99.93
2.2-2.26	0.2711	141	0.2093	2623	X-RAY DIFFRACTION	99.96
2.26-2.34	0.2221	148	0.2069	2615	X-RAY DIFFRACTION	100
2.34-2.42	0.2389	143	0.2038	2656	X-RAY DIFFRACTION	100
2.42-2.52	0.2194	151	0.1959	2608	X-RAY DIFFRACTION	99.96
2.52-2.63	0.2254	135	0.1949	2653	X-RAY DIFFRACTION	100
2.63-2.77	0.2236	134	0.1956	2672	X-RAY DIFFRACTION	100
2.77-2.94	0.2471	130	0.1902	2658	X-RAY DIFFRACTION	100
2.94-3.17	0.217	135	0.1886	2710	X-RAY DIFFRACTION	100
3.17-3.49	0.2072	152	0.1608	2710	X-RAY DIFFRACTION	100
3.49-3.99	0.1856	132	0.1397	2741	X-RAY DIFFRACTION	100
3.99-5.03	0.1482	129	0.1179	2836	X-RAY DIFFRACTION	100
5.03-79.83	0.173	148	0.1533	3056	X-RAY DIFFRACTION	99.78

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	2.45287806746	0.0147690763967	1.0713331325	0.126772935448	-0.0231875021458	4.09502563454	0.181026157446	0.129973148569	-0.230337296856	-0.0167738252735	-0.0435870359794	-0.0708254233386	0.358200524081	0.158746128649	-0.116342845956	0.183387851897	0.0208933975324	0.01920541737	0.142091978231	-0.0582633609771	0.240607179168	-16.2823858932	16.2947241646	-9.83124311574
2	5.58438117335	3.77024512059	5.60202479634	2.6741522067	3.89460417138	5.72582400422	0.176434692256	0.111198063071	-1.15783777679	0.426371070055	-1.15237166966	0.719585145125	1.82081930025	-1.21530397754	0.957282990665	0.68139914839	0.0386253467125	0.0913898500765	0.78005206951	-0.281650949574	0.806908229426	-9.60561301435	4.86366444922	-17.7688395653
3	2.24814432973	0.119988804542	0.564872557732	1.26906872557	-0.106506119684	3.56412055496	0.0173135874549	0.393915249171	-0.291594669444	-0.220706632187	-0.00357181512173	-0.0523199952964	0.240010807685	0.0919445941637	-0.0214351437061	0.231984064127	0.0351497565721	0.0141628909437	0.201226076034	-0.0900775123526	0.24706087464	-20.3612294382	13.471784982	-17.6416939592
4	6.97467288407	3.18878374691	-2.47089444594	1.9874815089	-0.652852710503	2.01320514259	-0.374740603142	-0.859105362234	-0.940961077997	0.435138075483	0.424606360184	0.442816041221	0.233977009974	-0.368353241195	-0.0117494049758	0.446837850847	0.0068524139416	0.0616132126941	0.450944937134	0.136774538806	0.46707831002	-24.7022530333	8.43515946489	11.1401846118
5	4.27152940367	-4.1509525088	2.28733628315	4.05613244117	-2.4678357095	7.5826084756	-0.0327119952138	-0.137595799106	-0.911311540692	0.0179044369415	0.0248534048382	0.224976838097	0.674431387724	-0.585048623325	-0.0792581833038	0.394617101924	-0.0780804420002	0.0260053356565	0.277542714176	0.040336800651	0.426461289388	-24.2193013587	5.59114341371	3.36513544729
6	7.55707013315	-0.557240329713	-4.92462996272	0.740586239589	-1.11854895246	6.93329042944	0.161270677032	0.553076169	0.30621301642	-0.303260568402	0.0870867156772	0.1764074293	-0.0582068648247	-0.453855047463	-0.191592451917	0.303630464492	0.0212733814327	-0.0343376469129	0.309529067578	-0.02683212409	0.256068658321	-35.5003604503	25.3062848859	-20.7272948131
7	4.26749945471	1.55577048646	1.22929986377	2.09693284374	0.130114153614	2.72024414531	-0.00556074409333	0.0976225515274	-0.0118596513017	-0.00604363090016	-0.0510367305136	-0.00868806872366	0.0445298419745	0.00944339037044	0.0807077818962	0.172429379942	0.0105815616483	0.0181160923409	0.118769176501	-0.0331414737462	0.170963172655	-23.9328728529	26.4264825845	-6.78608342854
8	6.57705958279	-3.05182292576	3.72613097912	3.52253720796	-3.59300097793	3.91559790465	0.0554428886276	-0.202814800139	0.810938116344	-0.412539644891	-0.130841273008	0.0477171934413	-0.447982336583	-0.506973501157	0.0941599716331	0.320291925847	0.0689647111804	0.0938362133508	0.332717699418	-0.0340434019915	0.408489910817	-35.9752737531	38.2717729538	-3.84689719033
9	2.07121625301	0.0375807564756	0.393028108882	0.524025884619	-0.544862377337	2.17183198716	-0.0101435031989	0.196716689797	0.0222212170548	0.0189667397931	0.0698953395309	-0.0440740550284	0.0449882200792	0.0522075126419	-0.00674727520918	0.147578108441	0.0357885683541	0.0245209623357	0.156230248954	-0.0489595086926	0.197734808873	-24.5736178865	24.2989286564	-9.52801521922
10	5.5140939911	2.69564083836	0.560138757687	8.02391830643	0.00630491467935	6.00862252719	0.0112266692028	-0.945587122104	0.466703704465	0.878131098736	0.175473203544	0.552004588349	-0.220528468653	-0.687335434951	-0.218375192888	0.270490328135	0.141376252294	0.0656304760289	0.498242807543	-0.0603790790646	0.297997755471	-29.1438384017	28.2183695044	11.2384065236
11	2.61002215337	0.192644642046	0.708628426786	2.43084222999	0.664982182881	2.75264222203	-0.0216907282206	-0.174889689058	0.0703277462988	-0.0337440516088	-0.151501774569	0.251330886952	0.00738823958207	-0.468585183761	0.101149511581	0.108699763063	-0.0135485615484	0.107362413601	0.204168254691	-0.0705252521721	0.234217774674	-31.5170357895	22.450207051	-4.88451040042
12	8.30728855176	-3.96799888438	3.62167815321	7.74423973916	-0.979632800513	2.67525540281	0.290813703362	-0.207622794802	-0.829111711443	-0.0434701913869	-0.1630696386	0.437394496561	1.12426540711	-0.994740402728	-0.106605265349	0.446401321903	-0.114034070406	0.0476503389494	0.484745158629	-0.126950089263	0.384371516681	-41.3016772966	12.7279299777	-11.9537848094

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 46 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 47 through 61 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 62 through 178 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 179 through 200 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 201 through 215 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1 through 11 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 12 through 46 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 47 through 61 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 62 through 124 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 125 through 148 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 149 through 196 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 197 through 216 )

-
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