PDB-6zsv: Structure of crocagin biosynthetic protein CgnB

ID or keywords:

Entry

Database: PDB / ID: 6zsv

Title

Structure of crocagin biosynthetic protein CgnB

Components

Uncharacterized protein

Keywords

PEPTIDE BINDING PROTEIN / crocagin / RiPP / RRE

Function / homology

metal ion binding / Uncharacterized protein

Function and homology information

Biological species

Chondromyces crocatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Koehnke, J. / Adam, S.

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 / Item: _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Feb 28, 2024	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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6zsv.cif.gz	431.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6zsv.ent.gz	302 KB	Display	PDB format
PDBx/mmJSON format	6zsv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6zsv_validation.pdf.gz	444.9 KB	Display	wwPDB validaton report
Full document	6zsv_full_validation.pdf.gz	472.2 KB	Display
Data in XML	6zsv_validation.xml.gz	24.5 KB	Display
Data in CIF	6zsv_validation.cif.gz	33.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zs/6zsv ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zsv	HTTPS FTP

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Related structure data

Related structure data	6zsuSC 7pd7C 8a2nC S: Starting model for refinement C: citing same article (ref.)
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

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

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

1

A: Uncharacterized protein

hetero molecules

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

2

B: Uncharacterized protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.448, 67.500, 86.152
Angle α, β, γ (deg.)	90.000, 95.990, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Uncharacterized protein Mass: 35466.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chondromyces crocatus (bacteria) / Gene: CMC5_025570 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: A0A0K1EBZ5
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.47 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 170 mM ammonium acetate, 85 mM sodium acetate pH 4.6, 25.5% PEG 4000 and 15% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.972422 Å / Relative weight: 1
Reflection	Resolution: 2.3→36.17 Å / Num. obs: 25752 / % possible obs: 96.5 % / Redundancy: 2.9 % / B_iso Wilson estimate: 42.4 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shell	Resolution: 2.3→2.38 Å / R_merge(I) obs: 0.454 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3773

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6ZSU

6zsu

Resolution: 2.3→36.17 Å / SU ML: 0.3465 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.3883 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.305	1339	5.24 %
R_work	0.2826	24219	-
obs	0.2838	25558	95.48 %

Solvent computation

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

Displacement parameters

B_iso mean: 67.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→36.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4834	0	4	61	4899

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0039	4920
X-RAY DIFFRACTION	f_angle_d	0.5589	6643
X-RAY DIFFRACTION	f_chiral_restr	0.0425	740
X-RAY DIFFRACTION	f_plane_restr	0.0034	867
X-RAY DIFFRACTION	f_dihedral_angle_d	14.7411	2965

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 (%)
2.3-2.38	0.3846	147	0.3739	2411	X-RAY DIFFRACTION	95.91
2.38-2.48	0.41	131	0.3719	2414	X-RAY DIFFRACTION	96.37
2.48-2.59	0.3649	128	0.3493	2363	X-RAY DIFFRACTION	92.84
2.59-2.73	0.3809	128	0.3444	2452	X-RAY DIFFRACTION	97.29
2.73-2.9	0.3802	123	0.3261	2432	X-RAY DIFFRACTION	96.2
2.9-3.12	0.373	136	0.3247	2439	X-RAY DIFFRACTION	96.19
3.12-3.44	0.2918	129	0.2918	2378	X-RAY DIFFRACTION	94.18
3.44-3.93	0.2911	152	0.2503	2458	X-RAY DIFFRACTION	97.24
3.93-4.95	0.2482	145	0.2394	2368	X-RAY DIFFRACTION	93.7
4.95-36.17	0.2696	120	0.2545	2504	X-RAY DIFFRACTION	94.97

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	6.47044998254	-1.5844012654	0.625340531092	4.62371302483	-0.615212887186	5.04211842224	0.0368769464563	-0.287871332689	-0.0734554826344	-0.0413090903858	0.0521999916325	-0.142090608836	0.0693009620172	0.210169145515	-0.0859633391528	0.245032264117	-0.00245740562889	0.00678978293214	0.456892358433	-0.0303824784605	0.33809484752	56.5462310161	61.3210927078	49.3818622313
2	4.87845412984	-0.210626199844	1.32171988209	2.13688339152	-0.423040153103	3.17860176438	-0.217552548575	-0.884638542357	0.453157641575	0.469703308001	0.246366396838	0.120317084877	-0.389124092157	-0.953461017774	-0.0675265394629	0.495830564407	0.118161631034	-0.0114329093797	0.828045576605	-0.147807575249	0.39275537333	32.9907224703	67.6958099727	61.6764973019
3	1.59246073253	0.36754627185	-2.26750358758	6.07037738391	-0.0607857123445	3.23389413827	-0.310504991344	-1.36310074547	0.103525276312	0.452399520859	0.333387805169	-0.836138521721	-0.387096021081	0.52270402871	-0.0120381009308	0.510055972754	0.0198824188891	-0.0299206368785	0.951119410449	-0.0918936767729	0.3348070751	46.8633231892	60.8519382267	59.8263693035
4	6.06555655003	-0.0815264345134	-1.59235319418	1.55112970383	-1.25361746212	3.6499224087	0.0194043698692	0.428379043115	-0.042578629985	-0.129125111281	0.0568349093258	0.0727289575002	0.0151941632385	-0.982737187651	-0.0922608409239	0.357651609007	-0.0325545923423	0.00255130512538	0.943587508353	-0.0506712176079	0.343974150668	28.2551460788	61.1776195685	42.7300188414
5	3.26240170408	1.5780562562	0.289089944616	2.04649921476	-1.39212375433	2.98546980772	-0.000467462197222	-0.146772753752	0.184847929138	-0.298652892136	-0.17353003703	-0.000809472926211	-0.16502188409	-0.530679967078	0.09836697298	0.321898504809	0.110257735918	0.00521809488718	0.599332630279	-0.00479464250606	0.373650488304	35.605972335	64.9330784644	47.3264490568
6	4.46618735324	1.99646024531	-0.844071654279	2.7864916089	-1.82313415164	2.97147785333	0.0896426779257	-0.406883773103	0.415757010312	-0.0524769859215	0.0828730917511	-0.181562820525	-0.562753044789	-0.361745800948	-0.175715465149	0.224211465449	0.149147422392	-0.0479685255518	0.694328191907	0.0349713213351	0.326591947111	33.4011325698	65.3194170088	49.7458077847
7	3.03888509012	-2.19336126858	1.45047326048	6.10644554434	-4.91394224235	7.68891862795	-0.580793501403	-0.529748685941	0.15691056186	1.13620898469	0.310133834607	0.332123065132	-2.49117866323	-0.375640316355	0.487155799505	0.61256794493	0.0115387559944	-0.162475037035	0.750910156772	-0.0273195810235	0.478817650087	47.7127433829	34.191467658	87.9222665202
8	8.24342326973	1.67651262784	-0.436149162555	5.49511336583	-1.10221840654	4.21216894795	0.00656097024015	0.532836868211	-0.202125254339	-0.10551805533	0.245289929933	0.197306594674	0.348535181079	0.923078204613	-0.0792671086171	0.387278194975	0.0565570233041	-0.0332630400044	0.62485523564	0.0132492311135	0.417420540701	49.9649925508	25.4244052303	72.0384711512
9	5.26284450093	-1.40974618295	-0.931038352454	3.0023276177	-0.882567799647	3.58937268498	0.0272171812938	0.400155974551	-0.103416077235	-0.187199252902	-0.253101537086	-0.0790129680162	-0.0977835003719	0.550286849789	0.209422261241	0.402210544019	0.0322892488108	0.0225136720429	0.694612165992	0.027246870247	0.360398506248	41.2183799524	29.4254148585	72.0720500541
10	4.17280069575	-0.0357666236985	0.408203085041	1.30902253398	-0.684334511744	2.58649076506	0.195229052879	-1.3479180433	0.115808939684	0.371781023549	0.111206414444	0.0887450405433	-0.43083164774	-0.210455308477	-0.27159063725	0.532706543143	0.020671401353	0.0111823296366	0.977118426628	-0.188311252712	0.39192603068	23.5384159538	34.5605163441	85.9082178283
11	2.55616330616	2.80246467583	-2.18594587038	6.00424436728	-0.52266894286	3.1798788664	0.262689198716	-1.23521839732	-0.270555614848	0.0991053567303	-0.153322415986	-0.761041170801	0.32346127912	1.18108074588	0.0278633255658	0.402091548879	0.00529929625177	0.0236325012017	0.827486464717	-0.0394745409375	0.318745190861	37.106510653	27.8462850719	83.7345349176
12	4.92802768029	-0.746255988714	-0.449288739104	0.691854284997	-1.09593613367	3.51780206194	0.144249234149	0.396216319229	-0.168391421317	-0.0674750705865	-0.0920410550679	0.0876625492789	0.159297926064	-0.480664905705	-0.0405044536791	0.374846943571	0.0401567759072	0.00356110945818	0.682681899081	-0.0530136216291	0.337499821615	20.4916058321	28.8318613874	68.3078854573
13	6.65566085363	1.71273893586	0.0715347118982	3.28179480766	0.532336316357	4.58617973309	0.333200075861	0.0858630607514	0.0816245160047	0.273753654883	-0.11605482576	0.0612250248765	-0.137033708578	0.0979248207512	-0.198786729765	0.291499527538	0.030973161978	-0.00702566391292	0.416616583324	0.0135514408622	0.249323177193	23.6989546474	32.0358910579	73.9097052184

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 101 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 102 through 145 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 146 through 165 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 166 through 241 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 242 through 270 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 271 through 303 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -6 through 11 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 12 through 66 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 67 through 101 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 102 through 146 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 147 through 165 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 166 through 270 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 271 through 303 )

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