PDB-3exb: Crystal structure of Cytochrome C Peroxidase with a Proposed Elec...

ID or keywords:

Entry

Database: PDB / ID: 3exb

Title

Crystal structure of Cytochrome C Peroxidase with a Proposed Electron Pathway Excised in a Complex with a Peptide Wire

Components

Cytochrome c peroxidase
N-[3-(1H-BENZIMIDAZOL-1-YL)PROPANOYL]GLYCYL-L-ALANYL-L-ALANINAMIDE

Keywords

OXIDOREDUCTASE/PEPTIDE / Oxidoreductase / Peroxidase / Heme / Hydrogen peroxide / Iron / Metal-binding / Mitochondrion / Transit peptide / OXIDOREDUCTASE-PEPTIDE COMPLEX

Function / homology

Function and homology information

cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Putnam, A.-M.A. / Lee, Y.-T. / Goodin, D.B.

Citation

Journal: Biochemistry / Year: 2009
Title: Replacement of an electron transfer pathway in cytochrome c peroxidase with a surrogate peptide
Authors: Hays Putnam, A.M. / Lee, Y.T. / Goodin, D.B.

History

Deposition	Oct 16, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 13, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2	Dec 12, 2012	Group: Other
Revision 1.3	Nov 11, 2020	Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary Category: pdbx_entity_src_syn / struct ...pdbx_entity_src_syn / struct / struct_conn / struct_conn_type / struct_ref_seq / struct_ref_seq_dif / struct_site Item: _struct.pdbx_descriptor / _struct_conn_type.id ..._struct.pdbx_descriptor / _struct_conn_type.id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Oct 20, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Remark 650

HELIX DETERMINATION METHOD: AUTHOR

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3exb.cif.gz	88.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3exb.ent.gz	65.6 KB	Display	PDB format
PDBx/mmJSON format	3exb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3exb_validation.pdf.gz	799.5 KB	Display	wwPDB validaton report
Full document	3exb_full_validation.pdf.gz	800.5 KB	Display
Data in XML	3exb_validation.xml.gz	8.4 KB	Display
Data in CIF	3exb_validation.cif.gz	14 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ex/3exb ftp://data.pdbj.org/pub/pdb/validation_reports/ex/3exb	HTTPS FTP

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Related structure data

Related structure data	1kxnS 1kxm S: Starting model for refinement
Similar structure data	1bes-d 1cpd-d 1aef-d 7ccp-d 1cck-d 1aeg-d 4jpt-d 2icv-d 2pcb-2 3ccp-d 2y5a-d 1ccl-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	#17 - May 2001 Cyclooxygenase similarity (1)

Deposited unit

A: Cytochrome c peroxidase

B: N-[3-(1H-BENZIMIDAZOL-1-YL)PROPANOYL]GLYCYL-L-ALANYL-L-ALANINAMIDE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	107.029, 75.070, 50.790
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Cytochrome c peroxidase / CCP Mass: 33589.383 Da / Num. of mol.: 1 / Fragment: sequence database residues 72-362 / Mutation: P190G, W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCP1, CCP, CPO / Plasmid: PT7CCP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Protein/peptide	N-[3-(1H-BENZIMIDAZOL-1-YL)PROPANOYL]GLYCYL-L-ALANYL-L-ALANINAMIDE Type: Peptide-like / Class: Inhibitor / Mass: 387.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) References: N-[3-(1H-benzimidazol-1-yl)propanoyl]glycyl-L-alanyl-L-alaninamide
#3: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 386 / 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: 3.05 Å³/Da / Density % sol: 59.71 %
Crystal grow	Temperature: 282 K / Method: vapor diffusion / pH: 6 Details: 200 mM KPi, 25% MPD, pH 6.0, VAPOR DIFFUSION, temperature 282K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 Å
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.08 Å / Relative weight: 1
Reflection	Resolution: 1.6→23.47 Å / Num. all: 54795 / Num. obs: 54328 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / B_iso Wilson estimate: 26.9 Å² / R_merge(I) obs: 0.074 / R_sym value: 0.074 / Net I/σ(I): 18.4
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.302 / Mean I/σ(I) obs: 2.5 / Num. measured all: 12322 / Num. unique all: 3857 / R_sym value: 0.302 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.1.9	data scaling
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
Blu-Ice		data collection
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1KXN

1kxn

Resolution: 1.6→10 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.958 / WR_factor R_free: 0.183 / WR_factor R_work: 0.161 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.903 / SU B: 2.9 / SU ML: 0.045 / SU R Cruickshank DPI: 0.073 / SU R_free: 0.073 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Also TLS refinement was employed.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19	2739	5.1 %	RANDOM
R_work	0.168	-	-	-
obs	0.169	54073	99.2 %	-
all	-	54758	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 83.01 Å² / B_iso mean: 17.819 Å² / B_iso min: 2.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	0 Å²	0 Å²
2-	-	0.29 Å²	0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→10 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2356	0	43	386	2785

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	2498
X-RAY DIFFRACTION	r_angle_refined_deg	1.344	2.011	3399
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.475	5	295
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.26	24.923	130
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.842	15	402
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	26.474	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	332
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	1990
X-RAY DIFFRACTION	r_mcbond_it	0.581	1.5	1447
X-RAY DIFFRACTION	r_mcangle_it	0.942	2	2323
X-RAY DIFFRACTION	r_scbond_it	1.762	3	1051
X-RAY DIFFRACTION	r_scangle_it	2.697	4.5	1073

LS refinement shell

Resolution: 1.6→1.64 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.356	177	-
R_work	0.344	3589	-
all	-	3764	-
obs	-	3464	96.02 %

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	9.4224	3.9467	0.9881	9.9951	3.4478	9.1101	0.0902	-1.2161	0.5064	0.8433	-0.0888	-0.2222	-0.2448	0.0396	-0.0014	0.1966	0.0551	-0.0014	0.2871	-0.0317	0.1373	9.779	88.62	71.025
2	7.2148	0.5993	-1.1412	5.4018	2.4465	7.3927	-0.1976	-0.2004	-0.1865	0.1665	0.072	0.3591	0.2976	-0.2013	0.1257	0.0373	0.0347	0.0071	0.1278	0.0467	0.1536	-1.65	84.931	55.964
3	4.382	-3.1662	-1.0846	7.6774	1.4071	16.9805	-0.2059	0.5677	-0.2158	-0.0429	0.0515	0.705	-0.0043	-0.7114	0.1543	0.0265	0.0137	-0.0172	0.1314	0.0082	0.1349	0.484	84.029	48.001
4	4.741	2.3463	-1.7964	7.5714	-1.7078	5	-0.152	0.5468	0.2451	-0.3055	0.1271	0.2111	-0.271	-0.1763	0.025	0.0465	0.0021	-0.0308	0.1537	0.0381	0.0935	8.752	88.747	40.794
5	19.1482	3.9938	0.7671	5.2807	-0.1071	4.6734	-0.123	1.1157	0.6328	-0.4996	0.0906	0.2098	-0.1909	0.015	0.0323	0.1786	-0.0031	-0.019	0.1945	0.0832	0.1474	19.503	96.715	35.036
6	1.4168	-0.1152	0.164	0.9691	-0.2822	1.9414	-0.0409	-0.1494	0.2906	0.1393	0.0266	0.0112	-0.2799	-0.0259	0.0143	0.0713	0.0205	-0.012	0.0975	-0.008	0.123	18.039	93.211	58.236
7	9.682	1.776	-1.9981	5.2699	-4.1549	8.9928	-0.002	0.1013	1.0775	-0.064	0.0383	0.1633	-0.6516	-0.3535	-0.0363	0.1778	0.052	-0.021	0.101	-0.0108	0.3208	17.67	104.978	58.781
8	5.7176	1.6586	4.5853	3.2799	1.095	10.0194	-0.1674	0.2	0.5298	0.0093	0.0397	-0.0262	-0.3558	0.2623	0.1278	0.0929	0.0129	0.009	0.0668	0.0199	0.2335	20.485	101.161	52.053
9	22.1615	0.2068	-5.0518	2.1212	-3.8773	8.0738	0.0735	0.204	0.9334	0.1427	0.0345	0.2931	-0.6319	-0.1243	-0.1081	0.1513	0.0343	-0.0192	0.0982	0.0295	0.2029	6.995	98.085	46.356
10	2.282	-0.2074	0.3296	0.8964	-0.2218	1.2707	-0.0346	-0.1032	0.1402	0.0758	0.0377	0.003	-0.0584	-0.012	-0.003	0.044	0.0084	0.004	0.0636	0.003	0.0584	20.113	88.245	56.908
11	9.6712	2.0918	4.3352	9.7744	2.8015	6.141	-0.1996	0.3658	0.8844	-0.3158	0.1184	0.2577	-0.4463	0.1461	0.0812	0.0787	-0.0216	-0.0098	0.14	0.0785	0.2185	30.806	100.771	46.139
12	16.7199	14.8713	9.4016	15.644	9.6496	5.9723	-0.8948	1.4358	-0.2592	-1.4696	1.1311	-0.4215	-0.5387	0.6416	-0.2363	0.2122	-0.0428	0.0007	0.2457	0.0367	0.2122	33.296	94.838	42.707
13	6.9823	-1.575	2.0452	2.4292	-0.0409	0.6843	-0.0105	0.72	0.1047	-0.4004	0.0385	-0.1875	-0.0101	0.2155	-0.0279	0.0825	-0.0093	0.0199	0.1383	0.0061	0.0797	32.892	81.204	43.566
14	7.1706	0.2496	0.6638	11.6782	1.3207	2.9366	-0.141	0.2662	0.2332	-0.1625	0.0942	-0.2134	-0.0509	0.0357	0.0468	0.0372	-0.0463	0.0035	0.1743	0.0366	0.1108	43.632	95.608	47.201
15	29.535	5.7705	12.1526	16.1526	3.8245	23.7687	0.1858	1.6509	-1.0254	-1.0716	0.0898	-0.3036	0.8116	0.0506	-0.2757	0.2055	-0.0238	0.018	0.2697	0.002	0.1502	40.951	89.429	38.837
16	3.1127	-0.6043	0.5733	5.2439	-1.0755	2.7087	-0.0405	-0.0314	0.0106	0.0346	-0.0315	-0.3952	0.0868	0.2025	0.072	0.007	-0.0008	0.0086	0.1228	-0.007	0.0578	38.57	82.177	53.868
17	7.8939	-4.8179	-3.6358	7.7861	4.4015	7.5184	0.1021	0.0979	-0.3144	-0.0973	-0.0487	0.037	0.2691	-0.0611	-0.0535	0.03	-0.0071	-0.0058	0.0792	0.0141	0.0375	26.853	73.645	48.79
18	5.8639	-2.3749	-2.3956	1.8197	3.0786	6.1601	-0.0558	-0.0907	-0.1605	0.222	0.0597	0.1032	0.264	-0.2323	-0.004	0.0323	0.0081	-0.0085	0.0995	0.0184	0.0551	16.711	82.125	59.701
19	18.3157	7.8218	4.1571	12.7654	5.9714	11.5009	0.355	-1.2564	-0.6717	0.7661	-0.2221	0.3119	0.6343	-0.6837	-0.133	0.1458	0.0037	0.0318	0.2357	0.0758	0.1883	3.688	78.28	65.101
20	2.836	-0.179	0.0598	1.714	1.3507	11.0116	-0.0467	0.2033	-0.1303	-0.0957	-0.0275	0.1556	0.4083	-0.0944	0.0741	0.0313	0.0017	-0.0083	0.1115	-0.0038	0.1103	7.313	78.517	44.112

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 8
2	X-RAY DIFFRACTION	2	A	9 - 16
3	X-RAY DIFFRACTION	3	A	17 - 21
4	X-RAY DIFFRACTION	4	A	22 - 31
5	X-RAY DIFFRACTION	5	A	32 - 39
6	X-RAY DIFFRACTION	6	A	40 - 73
7	X-RAY DIFFRACTION	7	A	74 - 78
8	X-RAY DIFFRACTION	8	A	79 - 89
9	X-RAY DIFFRACTION	9	A	90 - 98
10	X-RAY DIFFRACTION	10	A	99 - 178
11	X-RAY DIFFRACTION	11	A	179 - 186
12	X-RAY DIFFRACTION	12	A	187 - 193
13	X-RAY DIFFRACTION	13	A	194 - 207
14	X-RAY DIFFRACTION	14	A	208 - 221
15	X-RAY DIFFRACTION	15	A	222 - 227
16	X-RAY DIFFRACTION	16	A	228 - 248
17	X-RAY DIFFRACTION	17	A	249 - 260
18	X-RAY DIFFRACTION	18	A	261 - 273
19	X-RAY DIFFRACTION	19	A	274 - 279
20	X-RAY DIFFRACTION	20	A	280 - 292

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