PDB-6zsu: Structure of crocagin biosynthetic protein CgnE

ID or keywords:

Entry

Database: PDB / ID: 6zsu

Title

Structure of crocagin biosynthetic protein CgnE

Components

CgnE

Keywords

PEPTIDE BINDING PROTEIN / crocagin / RiPP / RRE

Function / homology

Uncharacterized protein

Function and homology information

Biological species

Chondromyces crocatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Adam, S. / Koehnke, J.

Funding support

Germany, 1items

Citation

Journal: Nat.Chem. / Year: 2023
Title: Unusual peptide-binding proteins guide pyrroloindoline alkaloid formation in crocagin biosynthesis.
Authors: Adam, S. / Zheng, D. / Klein, A. / Volz, C. / Mullen, W. / Shirran, S.L. / Smith, B.O. / Kalinina, O.V. / Muller, R. / Koehnke, J.

History

Deposition	Jul 16, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 22, 2023	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.title ..._citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6zsu.cif.gz	416.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6zsu.ent.gz	289.2 KB	Display	PDB format
PDBx/mmJSON format	6zsu.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6zsu_validation.pdf.gz	426.3 KB	Display	wwPDB validaton report
Full document	6zsu_full_validation.pdf.gz	429.1 KB	Display
Data in XML	6zsu_validation.xml.gz	27.4 KB	Display
Data in CIF	6zsu_validation.cif.gz	41.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zs/6zsu ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zsu	HTTPS FTP

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Related structure data

Related structure data	6zsvC 7pd7C 8a2nC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CgnE

B: CgnE

70 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CgnE

defined by author
Evidence: gel filtration
35 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CgnE

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

Unit cell

Length a, b, c (Å)	70.400, 75.340, 112.440
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
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	CgnE / CgnE Mass: 34977.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chondromyces crocatus (bacteria) / Gene: CMC5_025530 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: A0A0K1ECI7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 2.15 Å³/Da / Density % sol: 42.91 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM MgCl2, 100 mM Tris pH 8.5 and 20% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97797 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97797 Å / Relative weight: 1
Reflection	Resolution: 2→45.06 Å / Num. obs: 41166 / % possible obs: 99.9 % / Redundancy: 12.7 % / B_iso Wilson estimate: 19.62 Å² / R_merge(I) obs: 0.117 / Net I/σ(I): 16.9
Reflection shell	Resolution: 2→2.05 Å / R_merge(I) obs: 0.409 / Mean I/σ(I) obs: 7 / Num. unique obs: 2997 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	phasing
PHENIX	1.13_2998	refinement
XDS		data reduction
SCALA		data scaling
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2→45.06 Å / SU ML: 0.1778 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 16.7198 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2018	2077	5.05 %
R_work	0.1562	39031	-
obs	0.1585	41108	99.91 %

Solvent computation

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

Displacement parameters

B_iso mean: 24.84 Å²

Refinement step

Cycle: LAST / Resolution: 2→45.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4597	0	0	509	5106

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0081	4681
X-RAY DIFFRACTION	f_angle_d	0.9091	6330
X-RAY DIFFRACTION	f_chiral_restr	0.0527	699
X-RAY DIFFRACTION	f_plane_restr	0.0058	846
X-RAY DIFFRACTION	f_dihedral_angle_d	12.7568	2752

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 (%)
2-2.05	0.2199	132	0.1776	2579	X-RAY DIFFRACTION	99.71
2.05-2.1	0.2038	122	0.1733	2567	X-RAY DIFFRACTION	99.81
2.1-2.15	0.2228	138	0.1596	2569	X-RAY DIFFRACTION	99.85
2.15-2.22	0.2198	123	0.1561	2587	X-RAY DIFFRACTION	99.89
2.22-2.29	0.2219	127	0.1567	2574	X-RAY DIFFRACTION	99.93
2.29-2.37	0.2048	140	0.1451	2554	X-RAY DIFFRACTION	99.96
2.37-2.47	0.1971	137	0.1466	2580	X-RAY DIFFRACTION	99.96
2.47-2.58	0.2022	151	0.1513	2580	X-RAY DIFFRACTION	100
2.58-2.71	0.2075	135	0.1573	2597	X-RAY DIFFRACTION	100
2.71-2.88	0.2145	157	0.1548	2568	X-RAY DIFFRACTION	99.93
2.88-3.11	0.1785	138	0.1582	2580	X-RAY DIFFRACTION	99.89
3.11-3.42	0.1855	162	0.1507	2602	X-RAY DIFFRACTION	99.93
3.42-3.91	0.1805	121	0.1403	2660	X-RAY DIFFRACTION	99.93
3.91-4.93	0.1673	132	0.1373	2660	X-RAY DIFFRACTION	100
4.93-45.06	0.2448	162	0.1897	2774	X-RAY DIFFRACTION	99.93

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	3.38706268497	1.27051683293	0.12118082837	3.91095162167	-1.43832857356	2.8375258532	0.085607825138	-0.375644766657	-0.103085987424	0.332643144809	-0.148905590333	-0.131460722532	0.0460423982796	0.0668338426741	0.0444204101427	0.20504571441	-0.0195012347144	-0.0259864849107	0.202172415024	0.0318654878822	0.0896696760644	75.2281552762	35.0444340693	89.0719114874
2	3.92381338906	1.3446619371	-0.572680571146	1.73381088171	0.644001093171	3.02202259134	-0.0231593399443	-0.0355084344123	-0.0642041005323	0.0585691677374	-0.0175922195651	-0.0603031458232	0.121393139002	0.0129891939978	0.0320174847378	0.138728492734	0.028578269663	-0.0294575172125	0.0736453838795	0.0309466433986	0.113075897683	74.4543517056	34.8322167083	78.9059471665
3	1.78794388238	-0.595151116269	-0.167519191776	1.67144585865	0.260500999295	3.04183668568	0.0533235791273	-0.0287544522618	0.301488208196	-0.161209838567	0.0371664957861	-0.0926410065294	-0.608705126668	-0.136800158711	-0.0995938125358	0.225870885631	0.0134902224396	0.0200900368897	0.102195302852	-0.0427097491548	0.190147073871	75.7379576614	58.0121359721	70.4288171466
4	3.12824872948	-1.16256647017	0.0536428806143	1.75825628371	-1.61214320579	6.4886743864	0.272357912719	-0.0342360014798	0.294209203828	0.214537608438	0.201291842003	0.157755672793	-0.843462031524	-1.13517979516	-0.265128614258	0.371778644941	0.0239835159886	0.0231291687305	0.213727891331	-0.0369542982937	0.258443086727	68.050441727	55.763497419	64.254031346
5	0.209680256995	-0.404637347561	0.330344366542	2.2166416753	-0.45086652079	2.75259665592	0.0352918802971	-0.0771255349042	0.0700433275708	0.0597660709862	0.0322688529463	0.180332693855	-0.206132647923	-0.419595103069	-0.0744150736815	0.0811019678306	0.00474343085268	0.011139408388	0.168308695517	-0.0157391212122	0.164967065732	70.6823451197	46.3617467463	67.9489243383
6	4.36977119614	5.90507931739	-3.17987801166	8.63715935662	-3.30780477192	5.67834438015	0.03034597654	0.125016153434	-0.624210573331	-0.176178786372	-0.117013692956	-0.665444577569	0.38297220831	0.170227007776	0.108187271414	0.222300202557	0.0296839082482	0.0425203065469	0.145300625403	-0.00661624981659	0.144200082006	80.8013155048	31.6624644024	58.5721568609
7	3.12823496533	-0.173033983013	0.0495448578376	2.77539657243	-0.0615053086943	2.89970149145	0.0648186805893	0.252898795572	-0.0994341004881	-0.390063356357	-0.0531905847133	-0.139226580585	0.285511652465	-0.221159082037	0.00594430263564	0.207807014531	-0.00420809578966	0.0239263345692	0.110302710246	0.00293771898707	0.10355127366	74.8347928356	42.8537152718	53.3317942126
8	1.59904788144	0.302888295638	0.196495190286	1.72215856728	0.153346535395	2.56700969489	0.00505328053857	-0.137899292763	0.0493062599334	-0.0520644441896	0.0152558655324	-0.217678328609	-0.171515842692	0.0444198196178	-0.0344646734136	0.101158292976	0.00250329339892	0.0295431832453	0.10376148767	-0.017313900596	0.1207017057	79.2004735961	46.0182715346	66.4377693737
9	2.79314372711	0.566578695653	-0.146380041245	2.11849929205	0.760581802245	2.47048561267	-0.0383606328072	0.152900239352	-0.125634256797	-0.0977622266104	-0.0055026319015	-0.0877911762812	0.0990246547056	0.0223883412061	0.0381164641421	0.125161453673	-0.00362999426461	0.000866225690108	0.114071690214	-0.0106869625081	0.119340260496	49.8143639458	19.9157990976	66.2662787445
10	1.53620431856	-0.406517095352	0.251980899598	1.62717142628	0.245783468886	2.07875702912	0.0392615641824	0.103031506624	0.111692394611	-0.0315132900681	-0.00573009121048	-0.021018512449	0.0693071830098	-0.00227553139125	-0.0387994650757	0.0788408445487	-0.0188020233542	0.0132940248488	0.101910458434	0.0109431672633	0.154390745493	38.2273030258	35.8357063384	78.9962560267

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 109 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 110 through 136 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 137 through 153 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 154 through 199 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 200 through 219 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 220 through 264 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 265 through 313 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 8 through 109 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 110 through 314 )

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