PDB-3foo: A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordi...

ID or keywords:

Entry

Database: PDB / ID: 3foo

Title

A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Monoclinic Form

Components

Soluble cytochrome b562

Keywords

ELECTRON TRANSPORT / Four Helix Bundle / Heme / Iron / Metal-binding / Transport

Function / homology

Function and homology information

electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.4 Å

Authors

Radford, R.J. / Tezcan, F.A.

Citation

Journal: J.Am.Chem.Soc. / Year: 2009
Title: A superprotein triangle driven by nickel(II) coordination: exploiting non-natural metal ligands in protein self-assembly
Authors: Radford, R.J. / Tezcan, F.A.

History

Deposition	Dec 30, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 14, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id
Revision 1.4	Dec 25, 2024	Group: Derived calculations / Structure summary Category: pdbx_entry_details / struct_conn / struct_conn_type

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	3fopC 2qlaS 256b S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2bcm-d 2jkn-4 1ut2-1 1ut2-3 2w5p-d 2jkn-1 2jkn-5 2jkn-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3fopC

2qlaS

256b

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#164 - Aug 2013 Serotonin Receptor similarity (4) #165 - Sep 2013 Designed Protein Cages similarity (4) #184 - Apr 2015 Glucagon similarity (4) #199 - Jul 2016 Monellin similarity (4) #217 - Jan 2018 Opioid Receptors similarity (4) #255 - Mar 2021 Cisplatin and DNA similarity (4)

Deposited unit

A: Soluble cytochrome b562

B: Soluble cytochrome b562

C: Soluble cytochrome b562

D: Soluble cytochrome b562

E: Soluble cytochrome b562

F: Soluble cytochrome b562

G: Soluble cytochrome b562

H: Soluble cytochrome b562

I: Soluble cytochrome b562

J: Soluble cytochrome b562

K: Soluble cytochrome b562

L: Soluble cytochrome b562

hetero molecules

150 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Soluble cytochrome b562

B: Soluble cytochrome b562

C: Soluble cytochrome b562

hetero molecules

defined by author
37.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Soluble cytochrome b562

E: Soluble cytochrome b562

F: Soluble cytochrome b562

hetero molecules

defined by software
37.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Soluble cytochrome b562

H: Soluble cytochrome b562

I: Soluble cytochrome b562

hetero molecules

defined by software
37.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Soluble cytochrome b562

K: Soluble cytochrome b562

L: Soluble cytochrome b562

hetero molecules

defined by software
37.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.339, 107.396, 102.051
Angle α, β, γ (deg.)	90.00, 105.52, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J
11	K	K
12	L	L

#1: Protein	Soluble cytochrome b562 / Cytochrome b-562 Mass: 11537.963 Da / Num. of mol.: 12 / Mutation: K59C, R62A, H63A, K77H, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-PXX / N-1,10-phenanthrolin-5-ylacetamide Mass: 237.257 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₄H₁₁N₃O
#4: Chemical	... ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ni
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.68 Å³/Da / Density % sol: 54.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% PEG2000, 0.2 M NaCl, 0.1 M TRIS, 3.3 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97607 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2008 Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)
Radiation	Monochromator: Side-scattering cuberoot I-beam bent single crystal; asymmetric cut 12.2 degs. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97607 Å / Relative weight: 1
Reflection	Resolution: 2.4→98.533 Å / Num. all: 56311 / Num. obs: 55485 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / R_merge(I) obs: 0.096 / R_sym value: 0.096 / Net I/σ(I): 6.464
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.552 / Mean I/σ(I) obs: 1.3 / Num. measured all: 21402 / Num. unique all: 8079 / R_sym value: 0.552 / % possible all: 97

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.2.25	data scaling
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
ADSC	Quantum	data collection
MOLREP		phasing

Refinement

Starting model: PDB entry 2QLA

2qla

Resolution: 2.4→98.53 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.893 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.817 / SU B: 18.152 / SU ML: 0.238 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.562 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.268	3980	7.2 %	RANDOM
R_work	0.209	-	-	-
all	0.213	57214	-	-
obs	0.213	55103	96.31 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 76.47 Å² / B_iso mean: 41.455 Å² / B_iso min: 14.49 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	0 Å²	0.11 Å²
2-	-	-0.15 Å²	0 Å²
3-	-	-	0.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→98.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9648	0	756	119	10523

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	10684
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1
X-RAY DIFFRACTION	r_angle_refined_deg	1.246	2.146	14484
X-RAY DIFFRACTION	r_angle_other_deg	0.317	3	2
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.06	5	1260
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.25	27.436	468
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.263	15	1800
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.467	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1524
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	8139
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	4830
X-RAY DIFFRACTION	r_nbd_other	0.093	0.2	2
X-RAY DIFFRACTION	r_nbtor_refined	0.278	0.2	7207
X-RAY DIFFRACTION	r_nbtor_other	0.324	0.2	2
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	229
X-RAY DIFFRACTION	r_metal_ion_refined	0.018	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.223	0.2	36
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.215	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	0.37	1.5	6543
X-RAY DIFFRACTION	r_mcbond_other	0.046	1.5	1
X-RAY DIFFRACTION	r_mcangle_it	0.63	2	10116
X-RAY DIFFRACTION	r_scbond_it	1.142	3	5036
X-RAY DIFFRACTION	r_scangle_it	1.714	4.5	4344

Refine LS restraints NCS

Ens-ID: 1 / Number: 804 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	MEDIUM POSITIONAL	0.38	0.5
2	B	MEDIUM POSITIONAL	0.38	0.5
3	C	MEDIUM POSITIONAL	0.39	0.5
4	D	MEDIUM POSITIONAL	0.42	0.5
5	E	MEDIUM POSITIONAL	0.39	0.5
6	F	MEDIUM POSITIONAL	0.33	0.5
7	G	MEDIUM POSITIONAL	0.41	0.5
8	H	MEDIUM POSITIONAL	0.4	0.5
9	I	MEDIUM POSITIONAL	0.34	0.5
10	J	MEDIUM POSITIONAL	0.37	0.5
11	K	MEDIUM POSITIONAL	0.34	0.5
12	L	MEDIUM POSITIONAL	0.37	0.5
1	A	MEDIUM THERMAL	0.34	2
2	B	MEDIUM THERMAL	0.4	2
3	C	MEDIUM THERMAL	0.37	2
4	D	MEDIUM THERMAL	0.37	2
5	E	MEDIUM THERMAL	0.4	2
6	F	MEDIUM THERMAL	0.41	2
7	G	MEDIUM THERMAL	0.39	2
8	H	MEDIUM THERMAL	0.36	2
9	I	MEDIUM THERMAL	0.33	2
10	J	MEDIUM THERMAL	0.4	2
11	K	MEDIUM THERMAL	0.38	2
12	L	MEDIUM THERMAL	0.41	2

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.332	271	-
R_work	0.271	3718	-
all	-	3989	-
obs	-	-	94.55 %

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	10.0482	2.294	0.3551	1.4693	0.1386	1.9623	0.0707	-0.2316	0.4307	0.018	0.0173	0.1059	-0.4738	-0.1837	-0.0879	-0.0526	0.1254	0.0275	-0.0767	0.0334	-0.1671	-35.361	15.524	-7.821
2	0.9061	-0.1413	0.771	7.7607	-3.0654	4.656	0.0412	0.062	-0.0146	-0.5264	-0.2413	-0.333	0.0806	0.3019	0.2001	-0.2373	0.008	0.0445	-0.1058	-0.0147	-0.2011	-7.3	2.977	-19.924
3	2.0653	-2.6801	-1.5539	4.3996	2.3362	4.7691	0.1427	-0.1256	-0.3092	-0.1017	-0.0081	0.3812	0.4989	-0.5615	-0.1347	-0.0869	-0.141	-0.1439	-0.0658	0.0824	-0.0995	-31.163	-16.985	-9.534
4	4.3684	3.6171	1.9746	4.1853	1.1236	2.1177	-0.0775	-0.2756	0.4039	0.1323	-0.1469	0.3511	-0.5055	-0.4755	0.2244	0.0182	0.1808	-0.0741	-0.0807	-0.0531	-0.1531	-21.496	17.822	15.04
5	3.6129	-0.7946	-3.1662	1.0274	1.4227	6.5818	-0.0621	-0.0472	-0.2754	0.0683	0.0175	0.0435	0.4039	-0.2552	0.0446	-0.2002	-0.0677	-0.0456	-0.1023	0.0793	-0.1221	-23.758	-14.958	16.027
6	1.7517	-2.6338	1.5354	6.7566	-2.0931	3.7193	-0.0714	0.2694	0.1198	0.0077	-0.0796	-0.3657	-0.1168	0.2805	0.1511	-0.2834	-0.0488	0.0312	-0.0433	-0.0171	-0.1763	3.353	-0.535	3.995
7	3.9639	-4.1078	1.4402	6.6689	-1.0556	2.5636	-0.0004	0.2869	0.2758	-0.2044	-0.1415	-0.3396	-0.3285	0.3036	0.142	-0.1117	-0.1372	-0.0403	-0.1242	0.0554	-0.1987	7.792	15.567	31.284
8	6.4714	-0.2272	-4.8943	0.8159	-0.0267	7.2519	-0.2838	0.0429	-0.3652	0.1279	0.0936	-0.0212	0.9217	0.0095	0.1902	0.0133	-0.0065	-0.0621	-0.2558	-0.0161	-0.1483	2.381	-16.775	33.202
9	4.2768	4.7345	1.539	6.3625	1.3609	2.5728	0.0386	-0.1808	0.3398	0.0772	-0.1467	0.3242	-0.0719	-0.4101	0.108	-0.2432	0.0087	0.0315	0.0064	0.0108	-0.1697	-20.584	4.32	43.336
10	12.3161	-0.9422	0.2648	0.9037	0.0962	2.2125	-0.0702	-0.0657	0.5476	0.0312	0.035	-0.0666	-0.3233	0.0849	0.0352	-0.0792	-0.0261	-0.0283	-0.2297	-0.0083	-0.2082	12.603	18.585	59.499
11	1.3879	1.5295	-0.3515	6.6122	-3.8068	4.2157	0.0091	0.1235	-0.2332	0.0515	-0.0644	-0.5099	0.2324	0.3997	0.0554	-0.2243	0.0953	-0.0516	-0.1104	-0.0209	-0.1089	19.39	-13.464	56.268
12	0.9964	-1.4556	-0.2735	5.2284	2.694	4.5227	-0.0079	-0.1458	-0.1371	0.0937	0.0192	0.3301	0.1752	-0.2675	-0.0113	-0.2695	-0.0006	0.0458	-0.0366	0.0916	-0.1437	-9.242	-3.872	68.886

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 106
2	X-RAY DIFFRACTION	2	B	1 - 106
3	X-RAY DIFFRACTION	3	C	1 - 106
4	X-RAY DIFFRACTION	4	D	1 - 106
5	X-RAY DIFFRACTION	5	E	1 - 106
6	X-RAY DIFFRACTION	6	F	1 - 106
7	X-RAY DIFFRACTION	7	G	1 - 106
8	X-RAY DIFFRACTION	8	H	1 - 106
9	X-RAY DIFFRACTION	9	I	1 - 106
10	X-RAY DIFFRACTION	10	J	1 - 106
11	X-RAY DIFFRACTION	11	K	1 - 106
12	X-RAY DIFFRACTION	12	L	1 - 106

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-Yorodumi

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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

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Yorodumi