PDB-6cun: Engineered Cytochrome c from Rhodothermus marinus (Rma TDE) bound...

ID or keywords:

Entry

Database: PDB / ID: 6cun

Title

Engineered Cytochrome c from Rhodothermus marinus (Rma TDE) bound to carbene intermediate (1-ethoxy-1-oxopropan-2-ylidene)

Components

Cytochrome c

Keywords

LYASE / Carbene transferase / silicon-carbon bond

Function / homology

Function and homology information

electron transfer activity / heme binding / metal ion binding
Similarity search - Function

Biological species

Rhodothermus marinus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.29 Å

Authors

Lewis, R.D. / Buller, A.R. / Arnold, F.H.

Funding support

United States, 3items

Organization	Grant number	Country
National Science Foundation (NSF, United States)	MCB-1513007	United States
National Science Foundation (NSF, United States)	CHE-1361104	United States
National Science Foundation (NSF, United States)	CBET-1403077	United States

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Catalytic iron-carbene intermediate revealed in a cytochromeccarbene transferase.
Authors: Lewis, R.D. / Garcia-Borras, M. / Chalkley, M.J. / Buller, A.R. / Houk, K.N. / Kan, S.B.J. / Arnold, F.H.

History

Deposition	Mar 26, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 27, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 11, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Jul 18, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0	Mar 10, 2021	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_1 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6cun.cif.gz	65.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6cun.ent.gz	46.3 KB	Display	PDB format
PDBx/mmJSON format	6cun.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6cun_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6cun_full_validation.pdf.gz	1 MB	Display
Data in XML	6cun_validation.xml.gz	8.3 KB	Display
Data in CIF	6cun_validation.cif.gz	10.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cu/6cun ftp://data.pdbj.org/pub/pdb/validation_reports/cu/6cun	HTTPS FTP

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Related structure data

Related structure data	6cukSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1p28-1 2fz5-d 6cuk-d 1k0k-d 2vyy-d 3ios-d 1ypr-2 6rix-1 2fax-d 4tn8-d Search similar-shape structures by Omokage search (details) 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	#36 - Dec 2002 Cytochrome c similarity (5) #111 - Mar 2009 Hydrogenase similarity (5) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (5) #177 - Sep 2014 Apoptosomes similarity (4) #137 - May 2011 Cytochrome bc1 similarity (4) #59 - Nov 2004 Photosystem II similarity (4) #22 - Oct 2001 Photosystem I similarity (1) #232 - Apr 2019 Proteins and Biominerals similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#36 - Dec 2002
Cytochrome c
similarity (5)
#111 - Mar 2009
Hydrogenase
similarity (5)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (5)
#177 - Sep 2014
Apoptosomes
similarity (4)
#137 - May 2011
Cytochrome bc1
similarity (4)
#59 - Nov 2004
Photosystem II
similarity (4)
#22 - Oct 2001
Photosystem I
similarity (1)
#232 - Apr 2019
Proteins and Biominerals
similarity (1)

Deposited unit

A: Cytochrome c

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	60.343, 60.343, 77.232
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Cytochrome c Mass: 14029.785 Da / Num. of mol.: 1 / Mutation: V75T, M100D, M103E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodothermus marinus (bacteria) / Gene: cytC / Production host: Escherichia coli (E. coli) / References: UniProt: B3FQS5
#2: Chemical	ChemComp-HEC / HEME C Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₄FeN₄O₄
#3: Chemical	ChemComp-CA1 / ETHYL PROPIONATE Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₀O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.89 Å³/Da / Density % sol: 57.49 % / Description: Rods
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.43-1.48 M (NH4)2SO4 300-400 mM NaSCN 1.5% isopropanol 2:1 ratio of Rma TDE (14 mg/mL in 20mM Tris HCl pH 7.5) to well solution Crystals were soaked in well solution supplemented with 40 mM ...Details: 1.43-1.48 M (NH4)2SO4 300-400 mM NaSCN 1.5% isopropanol 2:1 ratio of Rma TDE (14 mg/mL in 20mM Tris HCl pH 7.5) to well solution Crystals were soaked in well solution supplemented with 40 mM ethyl 2-diazopropanoate under aerobic conditions for 30 minutes, followed by addition of sodium dithionite (50 mM) and freezing with liquid nitrogen

Crystal

Density Matthews: 2.89 Å³/Da / Density % sol: 57.49 % / Description: Rods

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.43-1.48 M (NH4)2SO4 300-400 mM NaSCN 1.5% isopropanol 2:1 ratio of Rma TDE (14 mg/mL in 20mM Tris HCl pH 7.5) to well solution Crystals were soaked in well solution supplemented with 40 mM ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.29→38.62 Å / Num. obs: 39554 / % possible obs: 100 % / Redundancy: 19.4 % / Net I/σ(I): 21.4
Reflection shell	Resolution: 1.29→1.32 Å / Redundancy: 16.6 % / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6CUK

6cuk

Resolution: 1.29→38.62 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.961 / SU B: 1.211 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.042 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20234	1935	4.7 %	RANDOM
R_work	0.18095	-	-	-
obs	0.18192	39554	99.97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 22.775 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.52 Å²	0.26 Å²	0 Å²
2-	-	0.52 Å²	0 Å²
3-	-	-	-1.7 Å²

Refinement step

Cycle: 1 / Resolution: 1.29→38.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	847	0	50	100	997

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.02	919
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	848
X-RAY DIFFRACTION	r_angle_refined_deg	1.814	2.128	1251
X-RAY DIFFRACTION	r_angle_other_deg	1.014	3.002	1940
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.653	5	110
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.652	23.684	38
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.721	15	143
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.403	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	134
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	1010
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	167
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.899	1.236	446
X-RAY DIFFRACTION	r_mcbond_other	0.899	1.234	445
X-RAY DIFFRACTION	r_mcangle_it	1.43	1.845	554
X-RAY DIFFRACTION	r_mcangle_other	1.429	1.847	555
X-RAY DIFFRACTION	r_scbond_it	1.275	1.357	473
X-RAY DIFFRACTION	r_scbond_other	1.274	1.361	474
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.791	2.007	698
X-RAY DIFFRACTION	r_long_range_B_refined	5.108	15.785	1030
X-RAY DIFFRACTION	r_long_range_B_other	4.928	15.127	1016
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.29→1.323 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.266	149	-
R_work	0.259	2873	-
obs	-	-	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	10.0653	2.7467	-0.0211	8.241	-3.3225	5.423	-0.1446	0.6686	-0.0773	-0.5212	0.2366	0.2666	0.1288	-0.4079	-0.0919	0.0484	-0.0335	-0.014	0.1552	0.0058	0.047	17.2303	-26.9337	4.8625
2	4.3863	-0.3165	-0.2485	6.4546	0.8855	4.473	0.0447	-0.1583	0.0821	-0.1032	0.0097	0.1744	-0.188	-0.1334	-0.0544	0.0313	-0.0224	0.0152	0.1287	0.018	0.0685	18.7377	-25.7474	12.6089
3	10.0378	-3.4919	3.5162	6.5329	-4.4652	5.8441	0.044	0.1204	0.352	-0.1993	-0.0037	0.5333	-0.4808	-0.4322	-0.0403	0.202	0.063	-0.0776	0.1139	-0.0176	0.1424	26.9612	-9.4519	17.0459
4	5.3336	-3.9586	-1.0165	5.8	1.043	4.8828	0.0549	-0.1998	0.1701	0.0854	0.0161	-0.2209	-0.1287	0.3135	-0.071	0.039	-0.0116	0.0013	0.1098	-0.0042	0.0406	38.3699	-17.7401	16.001
5	4.2465	-0.3331	2.2406	2.9721	-1.3593	2.5696	-0.0159	0.2646	-0.0548	-0.0551	-0.168	-0.1291	0.0259	0.4437	0.1839	0.0088	0.0184	-0.0004	0.142	0.0181	0.0485	40.9564	-22.7092	6.2165
6	2.4601	-5.7246	-0.2474	13.758	-0.9931	5.6596	0.2662	0.0077	0.1546	-0.6375	-0.2528	-0.3607	0.0473	0.8521	-0.0135	0.0616	-0.062	0.0586	0.3112	-0.0923	0.0661	40.5909	-19.3685	-0.4612
7	2.7741	-1.1711	-0.2446	4.4395	1.064	4.8138	-0.0364	0.2092	-0.0946	-0.0282	0.0438	0.051	0.1552	0.2954	-0.0074	0.0422	-0.0018	0.0155	0.1248	-0.0158	0.0222	36.4363	-20.536	1.8374
8	6.4497	1.5157	0.8135	4.0628	1.5492	6.7918	-0.074	0.2775	0.3524	-0.2183	0.1097	0.0967	-0.3748	-0.1346	-0.0358	0.0502	0.0016	0.0019	0.1	0.0266	0.0346	27.8406	-16.136	1.6384
9	2.1827	0.7481	-1.1148	1.7758	-1.7412	3.455	-0.0533	0.1632	-0.0012	-0.026	0.1286	0.0103	0.0562	-0.1952	-0.0753	0.0245	-0.0101	0.008	0.095	0.0019	0.0292	24.1794	-23.5277	7.4024
10	2.1433	1.6172	0.872	8.2498	3.2508	6.0682	-0.0014	0.2365	-0.4123	-0.0562	0.2029	-0.3583	0.4891	0.2242	-0.2015	0.0674	0.0075	0.0071	0.0685	-0.0427	0.0863	27.9931	-32.0228	8.943
11	7.0644	1.1515	-0.1459	12.2722	-0.0956	9.3772	0.103	0.055	-0.4977	-0.0698	0.0504	0.486	0.6505	-0.1544	-0.1533	0.0979	-0.0576	-0.0014	0.119	-0.0456	0.083	23.5408	-33.0748	1.9011
12	13.4789	0.6646	1.0685	7.6162	0.6169	12.0073	-0.1788	0.2084	-0.3646	-0.5251	0.0431	0.0826	0.2095	0.0825	0.1357	0.1286	-0.0245	0.0162	0.1137	-0.0618	0.0434	30.0158	-31.8968	-3.9737
13	0.5571	-0.7082	-2.0881	0.9764	2.6224	7.9267	-0.22	-0.3017	-0.0263	0.2529	0.2574	0.0112	0.6331	1.3084	-0.0374	0.1406	-0.0347	0.1138	0.5033	-0.1411	0.165	35.926	-31.5832	6.4052
14	1.0846	0.9258	0.1992	5.196	-2.3273	4.6826	0.0611	-0.0102	-0.0276	0.1285	-0.0168	0.074	-0.0125	-0.0134	-0.0443	0.0526	0.0095	0.0091	0.0715	-0.0044	0.0344	29.9268	-19.323	15.9354
15	11.6971	-7.0258	2.521	5.5859	2.8453	16.758	0.1854	0.6556	0.8283	-0.4429	-0.1829	-0.3287	-1.5216	0.4677	-0.0025	0.2124	0.0383	0.1186	0.1213	0.1781	0.3112	30.6678	-9.9729	8.1959

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 15
2	X-RAY DIFFRACTION	2	A	16 - 25
3	X-RAY DIFFRACTION	3	A	26 - 33
4	X-RAY DIFFRACTION	4	A	34 - 44
5	X-RAY DIFFRACTION	5	A	45 - 50
6	X-RAY DIFFRACTION	6	A	51 - 55
7	X-RAY DIFFRACTION	7	A	56 - 61
8	X-RAY DIFFRACTION	8	A	62 - 66
9	X-RAY DIFFRACTION	9	A	67 - 74
10	X-RAY DIFFRACTION	10	A	75 - 83
11	X-RAY DIFFRACTION	11	A	84 - 89
12	X-RAY DIFFRACTION	12	A	90 - 95
13	X-RAY DIFFRACTION	13	A	96 - 105
14	X-RAY DIFFRACTION	14	A	106 - 117
15	X-RAY DIFFRACTION	15	A	118 - 123

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