PDB-5xed: Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT ...

ID or keywords:

Entry

Database: PDB / ID: 5xed

Title

Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins

Components

Cytochrome c-551,Cytochrome c-552
Cytochrome c-552,Cytochrome c-551

Keywords

ELECTRON TRANSPORT /

Chimeric protein

Function / homology

Function and homology information

electron transfer activity /

periplasmic space / iron ion binding /

heme binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Hydrogenobacter thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Zhang, M. / Nakanishi, T. / Yamanaka, M. / Nagao, S. / Yanagisawa, S. / Shomura, Y. / Shibata, N. / Ogura, T. / Higuchi, Y. / Hirota, S.

Funding support

Japan, 3items

Citation

Journal: Chembiochem / Year: 2017
Title: Rational Design of Domain-Swapping-Based c-Type Cytochrome Heterodimers by Using Chimeric Proteins.
Authors: Zhang, M. / Nakanishi, T. / Yamanaka, M. / Nagao, S. / Yanagisawa, S. / Shomura, Y. / Shibata, N. / Ogura, T. / Higuchi, Y. / Hirota, S.

History

Deposition	Apr 4, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 9, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5xed.cif.gz	81.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xe/5xed ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xed	HTTPS FTP

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Related structure data

Related structure data	5xecC 1ynrS 351cS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5xec-d 5yam-d 4wvt-d 1ggw-d 1t0z-8 2hax-d 4e50-d 3vym-1 5ujl-d 5x7b-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-551,Cytochrome c-552

C: Cytochrome c-552,Cytochrome c-551

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	32.088, 65.912, 35.380
Angle α, β, γ (deg.)	90.00, 103.72, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cytochrome c-551,Cytochrome c-552 / Cytochrome C8 / Cytochrome c551 / Cytochrome c552 Mass: 8726.040 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-42,UNP RESIDUES 37-98 / Mutation: M61A Source method: isolated from a genetically manipulated source Details: The chimeric protein of Cytochrome c-551 (23-42) and Cytochrome c-552 (37-98) Source: (gene. exp.) Pseudomonas aeruginosa (bacteria), (gene. exp.) Hydrogenobacter thermophilus (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1, DSM 6534 / IAM 12695 / TK-6 Gene: nirM, PA0518, HTH_0988, Hydth_0984 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: P00099, UniProt: P15452
#2: Protein	Cytochrome c-552,Cytochrome c-551 / Cytochrome c552 / Cytochrome C8 / Cytochrome c551 Mass: 8504.748 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-36,UNP RESIDUES 43-104 Source method: isolated from a genetically manipulated source Details: The chimeric protein of Cytochrome c-552 (19-36) and Cytochrome c-551 (43-104) Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria), (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: DSM 6534 / IAM 12695 / TK-6, ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: HTH_0988, Hydth_0984, nirM, PA0518 / Production host: Escherichia coli (E. coli) / References: UniProt: P15452, UniProt: P00099
#3: Chemical	ChemComp-HEC / HEME C / Heme C Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₄FeN₄O₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.11 Å³/Da / Density % sol: 41.69 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES containing 25% w/v PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 13, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.55→50 Å / Num. obs: 21840 / % possible obs: 99.5 % / Redundancy: 3.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.044 / Net I/σ(I): 16.6
Reflection shell	Resolution: 1.55→1.58 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.533 / Mean I/σ(I) obs: 2 / Num. unique obs: 1164 / CC_1/2: 0.755 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 351C, 1YNR

351c

1ynr

Resolution: 1.55→34.37 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.925 / SU B: 3.347 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23758	979	4.9 %	RANDOM
R_work	0.20873	-	-	-
obs	0.21016	19118	96.57 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 19.105 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	-0 Å²	-0.16 Å²
2-	-	0.05 Å²	-0 Å²
3-	-	-	0.14 Å²

Refinement step

Cycle: 1 / Resolution: 1.55→34.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1208	0	86	67	1361

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	1332
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1277
X-RAY DIFFRACTION	r_angle_refined_deg	1.993	2.166	1828
X-RAY DIFFRACTION	r_angle_other_deg	0.922	3	2948
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.428	5	160
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.841	26.522	46
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.403	15	216
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	6.885	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	178
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.021	1516
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	254
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	0.794	0.832	646
X-RAY DIFFRACTION	r_mcbond_other	0.794	0.831	645
X-RAY DIFFRACTION	r_mcangle_it	1.282	1.245	804
X-RAY DIFFRACTION	r_mcangle_other	1.281	1.246	805
X-RAY DIFFRACTION	r_scbond_it	1.26	1.004	686
X-RAY DIFFRACTION	r_scbond_other	1.256	1.003	682
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.962	1.439	1023
X-RAY DIFFRACTION	r_long_range_B_refined	3.427	7.483	1651
X-RAY DIFFRACTION	r_long_range_B_other	3.386	7.357	1629
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	56	-
R_work	0.266	1078	-
obs	-	-	73.59 %

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	4.5812	-1.2958	-1.4093	5.623	0.0641	11.5922	0.0581	0.5363	-0.4053	0.0151	-0.0171	-0.1157	0.3504	0.019	-0.041	0.1616	0.0349	-0.0127	0.1605	-0.0369	0.1423	20.111	-2.1399	-1.7225
2	8.4237	0.4698	0.6491	2.4887	-0.9058	3.4268	0.1219	0.1776	-0.2983	-0.0131	-0.0172	-0.0473	0.3595	-0.0627	-0.1047	0.1096	-0.0178	-0.0218	0.0088	0.0027	0.055	14.0647	0.4289	6.8294
3	2.7591	-1.8163	1.719	4.3364	-3.0522	7.9603	-0.0476	-0.0447	0.1739	0.0266	-0.0366	-0.2528	-0.2303	0.2241	0.0842	0.0155	-0.0169	0.0054	0.0243	-0.0141	0.0822	1.051	-4.4951	21.8974
4	3.0746	0.1601	2.7126	0.4851	0.503	6.5287	0.1311	-0.2834	-0.0449	0.1395	-0.0248	-0.0341	0.134	0.0309	-0.1064	0.0999	0.0081	0.0044	0.0945	-0.0009	0.0688	-4.1335	-11.6159	33.1667
5	5.0405	1.8236	-1.5454	5.5699	-0.3598	0.9446	-0.1595	-0.0855	0.6098	0.1792	0.2437	0.3337	-0.3079	-0.0205	-0.0842	0.3061	0.0568	-0.0913	0.0543	-0.0269	0.1017	-9.4276	-2.4354	23.8228
6	4.0004	0.794	-0.3941	3.2496	-0.7219	1.0599	-0.0978	0.1374	-0.135	-0.1714	0.0238	0.1934	-0.0085	-0.1268	0.074	0.0144	0.0028	-0.0126	0.0195	-0.0188	0.0334	-10.8868	-12.4955	19.5045
7	7.2314	0.9462	-1.4793	1.7435	0.9838	1.1768	-0.0056	-0.1347	0.0983	-0.0572	0.0873	-0.1029	-0.0566	0.1335	-0.0817	0.0398	-0.0181	-0.0157	0.0643	0.0274	0.0604	2.8107	-12.4853	22.5446
8	4.1586	2.4673	1.6243	5.2582	0.8198	4.0391	-0.0024	0.5129	-0.4435	-0.3382	0.083	-0.6036	0.2981	0.3568	-0.0806	0.0556	0.0335	0.0433	0.0842	-0.0252	0.1031	-2.7389	-9.5448	12.1858
9	3.0193	-1.2547	1.3019	1.6754	-1.1123	8.6674	0.0592	-0.0875	-0.3264	-0.0562	0.025	0.1356	0.176	-0.1506	-0.0842	0.0183	-0.0277	-0.0008	0.0467	0.0002	0.0627	9.2823	6.8299	6.0101
10	12.4589	1.7246	4.5172	4.1054	-2.8859	4.8279	-0.0764	0.0029	0.2632	0.3737	-0.1248	-0.0676	-0.3943	0.1229	0.2012	0.1607	-0.0151	-0.0185	0.0796	0.0233	0.0545	12.2839	17.005	-2.6388
11	6.8864	4.7476	4.8004	8.2586	-3.5809	12.9003	-0.3317	0.2151	0.2644	-0.1631	0.0632	0.0774	-0.3543	0.2254	0.2685	0.0714	0.0213	0.0661	0.1001	0.0492	0.1296	20.8083	13.9146	3.2343
12	8.6159	1.0176	-1.9462	1.8765	-0.5604	3.6905	-0.0228	-0.4874	-0.2125	0.1898	-0.0088	-0.0103	0.0082	0.2311	0.0316	0.0227	0.0082	-0.0041	0.0342	0.0118	0.0416	18.3356	11.4232	12.4064
13	12.0984	3.5401	4.6252	1.2376	1.9792	3.739	-0.097	0.823	-0.1547	-0.0453	0.2667	-0.1017	-0.008	0.3531	-0.1697	0.2442	0.0204	0.0775	0.2865	-0.0877	0.2083	24.5874	7.7426	-2.2882
14	10.8818	3.3731	-0.3348	7.3688	-0.5174	5.2908	-0.0113	0.583	-0.0206	-0.2947	-0.013	0.0948	-0.0174	-0.0537	0.0243	0.091	0.0035	-0.013	0.0795	-0.0335	0.0238	12.3455	6.6651	-3.7215

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 8
2	X-RAY DIFFRACTION	2	A	9 - 21
3	X-RAY DIFFRACTION	3	A	22 - 36
4	X-RAY DIFFRACTION	4	A	37 - 42
5	X-RAY DIFFRACTION	5	A	43 - 60
6	X-RAY DIFFRACTION	6	A	61 - 77
7	X-RAY DIFFRACTION	7	A	78 - 82
8	X-RAY DIFFRACTION	8	C	1 - 19
9	X-RAY DIFFRACTION	9	C	20 - 31
10	X-RAY DIFFRACTION	10	C	32 - 40
11	X-RAY DIFFRACTION	11	C	41 - 47
12	X-RAY DIFFRACTION	12	C	48 - 63
13	X-RAY DIFFRACTION	13	C	64 - 72
14	X-RAY DIFFRACTION	14	C	73 - 80

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