PDB-7aba: The structure of the Bottromycin biosynthetic protein SalCYP

ID or keywords:

Entry

Database: PDB / ID: 7aba

Title

The structure of the Bottromycin biosynthetic protein SalCYP

Components

(SalCYP) x 2

Keywords

BIOSYNTHETIC PROTEIN / Bottromycin / cytochrome / P450

Function / homology

Cytochrome p450 / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha / HEME C

Function and homology information

Biological species

Salinispora tropica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85002316788 Å

Authors

Adam, S. / Koehnke, J.

Funding support

Germany, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2020
Title: Characterization of the Stereoselective P450 Enzyme BotCYP Enables the In Vitro Biosynthesis of the Bottromycin Core Scaffold.
Authors: Adam, S. / Franz, L. / Milhim, M. / Bernhardt, R. / Kalinina, O.V. / Koehnke, J.

History

Deposition	Sep 7, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 2, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 6, 2021	Group: Data collection / Database references / Structure summary Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_contact_author / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7aba.cif.gz	571.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7aba.ent.gz	392.1 KB	Display	PDB format
PDBx/mmJSON format	7aba.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7aba_validation.pdf.gz	561.9 KB	Display	wwPDB validaton report
Full document	7aba_full_validation.pdf.gz	564.9 KB	Display
Data in XML	7aba_validation.xml.gz	16 KB	Display
Data in CIF	7aba_validation.cif.gz	30.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ab/7aba ftp://data.pdbj.org/pub/pdb/validation_reports/ab/7aba	HTTPS FTP

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Related structure data

Related structure data	7abbC C: citing same article (ref.)
Similar structure data	2vr2-d 4z2l-d 3j4s-d 3nhb-d 2rim-d 5x0v-2 4dni-d 6lqo-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#36 - Dec 2002 Cytochrome c similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #137 - May 2011 Cytochrome bc1 similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #232 - Apr 2019 Proteins and Biominerals similarity (1) #59 - Nov 2004 Photosystem II similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: SalCYP

B: SalCYP

hetero molecules

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

1

A: SalCYP

hetero molecules

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

2

B: SalCYP

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.448, 97.403, 93.285
Angle α, β, γ (deg.)	90.000, 104.575, 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	SalCYP Mass: 44896.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salinispora tropica (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein	SalCYP Mass: 44896.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salinispora tropica (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-HEC / HEME C Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₄FeN₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1087 / 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: 2.44 Å³/Da / Density % sol: 49.54 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Calcium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.738 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.738 Å / Relative weight: 1
Reflection	Resolution: 1.85→48.825 Å / Num. obs: 74132 / % possible obs: 99.61 % / Redundancy: 28.7 % / B_iso Wilson estimate: 13.9747877323 Å² / R_merge(I) obs: 0.158 / Net I/σ(I): 18.9
Reflection shell	Resolution: 1.85→1.92 Å / R_merge(I) obs: 0.699 / Num. unique obs: 7163

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Processing

Software

Name	Version	Classification
Coot		model building
PHENIX	1.11.1_2575	refinement
Coot		model building
XDS		data reduction
SCALA		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.85002316788→48.8245361591 Å / SU ML: 0.15868485607 / Cross valid method: FREE R-VALUE / σ(F): 1.3364675622 / Phase error: 16.9464273921
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.175735614349	3674	4.956893644 %
R_work	0.141481864079	70445	-
obs	0.143185800858	74119	99.6089235318 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.7389141152 Å²

Refinement step

Cycle: LAST / Resolution: 1.85002316788→48.8245361591 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6294	0	0	1087	7381

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00519940387775	6487
X-RAY DIFFRACTION	f_angle_d	0.778763506845	8871
X-RAY DIFFRACTION	f_chiral_restr	0.0459405566595	919
X-RAY DIFFRACTION	f_plane_restr	0.00530337306021	1186
X-RAY DIFFRACTION	f_dihedral_angle_d	11.5619486509	3803

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 (%)
1.85003-1.8744	0.246788183359	118	0.199024043739	2524	X-RAY DIFFRACTION	92.0236851271
1.8744-1.9	0.203974658039	118	0.169568259633	2689	X-RAY DIFFRACTION	99.2925362575
1.9-1.9272	0.209268316834	131	0.160493017436	2712	X-RAY DIFFRACTION	99.964838256
1.9272-1.956	0.204627150714	142	0.157910009932	2713	X-RAY DIFFRACTION	99.8950314906
1.956-1.9865	0.196958744914	151	0.156424055981	2682	X-RAY DIFFRACTION	100
1.9865-2.0191	0.190609788493	122	0.150529977504	2768	X-RAY DIFFRACTION	99.8963014172
2.0191-2.0539	0.240761886027	123	0.14389662003	2693	X-RAY DIFFRACTION	99.9290276792
2.0539-2.0913	0.19926605775	146	0.142950053263	2709	X-RAY DIFFRACTION	99.9649859944
2.0913-2.1315	0.179454196487	147	0.139715201454	2691	X-RAY DIFFRACTION	99.9647763297
2.1315-2.175	0.176444012824	148	0.140904070343	2701	X-RAY DIFFRACTION	99.8948106592
2.175-2.2223	0.154909451222	167	0.13716789472	2681	X-RAY DIFFRACTION	99.9648999649
2.2223-2.274	0.172458736546	131	0.138483231276	2733	X-RAY DIFFRACTION	99.8605299861
2.274-2.3308	0.170872421508	152	0.134666779098	2721	X-RAY DIFFRACTION	99.9652052888
2.3308-2.3939	0.175886304351	134	0.132829934835	2708	X-RAY DIFFRACTION	100
2.3939-2.4643	0.189881971763	153	0.129617476284	2682	X-RAY DIFFRACTION	99.9647390691
2.4643-2.5438	0.159522551166	141	0.132185660508	2743	X-RAY DIFFRACTION	99.9653379549
2.5438-2.6347	0.161521038272	155	0.132882983195	2692	X-RAY DIFFRACTION	100
2.6347-2.7402	0.187407384636	158	0.134425187518	2704	X-RAY DIFFRACTION	99.9650716032
2.7402-2.8649	0.180927664523	153	0.137916119114	2704	X-RAY DIFFRACTION	99.9300454704
2.8649-3.016	0.15759138101	131	0.132712413729	2740	X-RAY DIFFRACTION	100
3.016-3.2049	0.160317605878	128	0.133293373024	2729	X-RAY DIFFRACTION	100
3.2049-3.4523	0.162536127519	140	0.134972468249	2726	X-RAY DIFFRACTION	100
3.4523-3.7996	0.139961829314	146	0.128470593369	2737	X-RAY DIFFRACTION	99.9653259362
3.7996-4.3491	0.141908043311	146	0.127360375082	2724	X-RAY DIFFRACTION	100
4.3491-5.4782	0.166762687195	145	0.134374609976	2760	X-RAY DIFFRACTION	99.9655884377
5.4782-48.823	0.238404613132	148	0.196253535618	2779	X-RAY DIFFRACTION	99.6255956433

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	0.898512935796	0.832591855648	0.851986719221	0.79532259909	0.37681755961	1.12140827436	-0.0919165936779	0.381831089635	-0.0279623418651	-0.154635146449	0.0181332726836	0.0723008740661	-0.105622959245	-0.124790931048	0.0508736277953	0.128933301221	0.0231986086843	-0.0106598324422	0.232826509314	-0.00844588977393	0.0971597348165	-21.3935641083	56.6483430809	47.3368240711
2	6.12965790478	0.512369471224	1.03266481174	4.80967618522	0.854187062269	5.74839878087	0.124128557203	0.140256207018	-0.187808930092	-0.0471217612988	-0.0179455387038	0.286842423765	0.351405121796	-0.232843190007	-0.00687772850716	0.0818902887546	0.00035111187075	-0.00567639925785	0.0515017166957	0.0167265417911	0.116438585744	-23.3121405159	44.9787588055	73.8322616554
3	0.79982814549	0.0672635661427	0.0382447986032	1.04353299282	0.0309719242873	0.695217587899	-0.0129070774303	-0.0330003557035	-0.112836882934	0.0217101924786	0.0237563140304	0.0357035805511	0.106314892539	0.00929060172378	-0.0050198397791	0.08445928355	0.00339755166848	-0.00304810645773	0.05238549336	0.0125425192845	0.0752059201336	-4.18394905891	43.7140306477	75.3866670719
4	1.47737294733	0.21667694421	0.431052076801	0.426079826861	0.114847539935	0.936030265315	-0.0371938297305	0.142181365652	0.0992859245423	-0.0332036848949	0.0076462367366	-0.0305781965368	-0.126189231155	0.0558247384633	0.0153667365591	0.0920383611816	-0.00800370185126	0.00243070285975	0.051335269678	0.0141636780312	0.0723803262479	-5.39775489082	61.6371056699	65.217938513
5	3.07753999498	-1.23591218943	-3.57420302944	2.40943564609	0.881356386585	4.30345385833	-0.681754782281	0.182347335107	-0.0324439650977	-0.102994415052	0.338888575074	-0.601356748683	0.157185627882	1.31695527305	0.300796514562	0.459933868848	0.012397831331	-0.0492441541627	0.838399550596	-0.108371114943	0.894791857419	-32.9755841628	42.9180710535	144.824771282
6	3.14163164125	-1.41820445067	-0.473175043951	2.44557793289	1.00393717705	4.42044459233	-0.0247622017863	-0.529024844529	0.112219508057	0.116159666647	0.030441406915	-0.0825149199985	0.0322984602175	-0.0732636542783	-0.0109657788934	0.0888261181326	-0.0268253664349	-0.00931850534839	0.185078834894	-0.00261897146741	0.0629093433225	-12.2403927034	49.5516303143	131.718793532
7	1.20274250113	0.122220242811	-0.246754273728	0.374686226437	-0.0886309230516	0.667092238552	0.037169797735	-0.0175309092733	0.110034084315	-0.017243282762	-0.0162057583824	0.0243200089714	-0.0288595837977	-0.0155431415492	-0.0233409719626	0.0758469086375	0.00483141895084	-0.00178537989364	0.0311552131015	-0.0106767392718	0.0704409570242	-8.25325965049	55.78487328	104.328168375
8	2.4412371592	0.083278756417	0.715050197792	3.91712414578	-0.391639069394	7.4734236786	0.063563299215	-0.193283468157	0.0483102648544	0.342119825495	-0.0411373760755	-0.111447042475	0.142801189224	0.192486735754	-0.0728114198344	0.094015144162	-0.00975439429652	-0.0101707088958	0.0549721073006	-0.00832294611465	0.145341872136	4.2278560867	69.1399934475	113.360449155
9	2.78848511092	0.296694606697	2.03703179312	2.31048993812	-0.195947725756	2.90698895423	-0.0378403879579	-0.0243229859602	0.191333037784	-0.186424293099	-0.0212714236415	0.16407782717	-0.162701793591	-0.124953205686	0.0581066978018	0.127866810797	0.0294920402705	0.0201335454451	0.0351972995036	0.00468608150954	0.125696584597	-13.5629792329	72.2184193887	98.8894089905
10	1.74680573916	-0.609465743484	0.141493282176	1.66017467075	-0.319516037017	0.752352784038	0.00690324366628	-0.00973442765936	-0.0528515506237	-0.0325190359805	-0.0262155737936	-0.209192883969	0.0708351300086	0.060725613603	0.0175046479011	0.0735064516952	-0.00299461451563	0.019474151107	0.0445118491263	0.00206771916662	0.0498655608321	-1.27142441177	47.7059271535	107.985461222
11	2.80842027655	-1.50118180678	-1.31011707105	2.34551263731	1.26625231606	2.161214017	-0.0287934067844	-0.111020056073	-0.189768736895	0.0750212133248	-0.0335827183025	0.109815532125	0.135824198757	-0.089480312545	0.0526780615055	0.0738747814393	-0.0180269341202	-0.0130397723353	0.0784538058189	0.0233620321343	0.0470920212269	-14.2216573402	44.1140651807	120.148181859
12	3.18547473133	-0.47086001375	-0.196941411833	0.622146154887	0.150251306365	0.816060739708	-0.00842434194315	-0.154409192338	-0.0280198637239	0.0326326762041	0.0108921937963	-0.0792791835996	0.049671020159	0.100867233553	-0.0132923816484	0.0845281152788	-0.00102100981536	0.00239046963092	0.0302140540918	0.0135892569702	0.0676447885868	3.30365761658	47.8182910842	109.414215104

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 88 through 111 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 112 through 265 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 266 through 400 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 20 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 21 through 60 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 61 through 162 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 163 through 193 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 194 through 233 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 234 through 290 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 291 through 344 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 345 through 400 )

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