1zzh

Structure of the fully oxidized di-heme cytochrome c peroxidase from R. capsulatus

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein homooligomer	Homooligomer	2 / 0 / 0 / 0	Consistent with protein count
2	Protein homooligomer	Homooligomer	2 / 0 / 0 / 0	Consistent with protein count
3	Protein homooligomer	Homooligomer	4 / 0 / 0 / 0	Consistent with protein count

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1zzh
Deposition date deposition_date	2005-06-14
Structure title title	Structure of the fully oxidized di-heme cytochrome c peroxidase from R. capsulatus
Keywords keywords	cytochrome c peroxidase, heme groups, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1zzh__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1zzh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zzh__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.34 Å
Rg (electron density)	26.60 Å
Total Rg	27.38 Å
Atom count	4547
Residues	595
Excluded volume	80681 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zzh__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zzh__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1zzh__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	cytochrome c peroxidase
Molecular weight formula_weight	34999.2 kDa
EC 编号 ec_number	1.11.1.5
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9290

EDAALREEAKGLFEVIPMQAPQLADNNTVTRDKIDLGAMLFFDPRMSKSGVFSCQSCHNVGLGGVDGLETSIGHGWQKGPRNAPTALNAVFNVAQFWDGRAPDLAAQAKGPVQAGVEMNNTPENLVATVQSMPGYVEAFAKAFPGQKDPISFDNFALAVEAFEATLITPNSKFDQWLMGADGAMSADEKAGLKLFIDTGCAACHNGINIGGNGYYPFGVVEKPGAEVLPAGDKGRFAVTATADDEYVFRAGPLRNIALTAPYFHSGKVWDLREAVSVMANSQLGATLDDTQVDQITAFLGTLTGEQPEVVHPILPVRSAQTPRPEHMN

Source Source

Source organism organism	Rhodobacter capsulatus
NCBI taxonomy ID ncbi_taxonomy_id	1061
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1zzha1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d1zzha2
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d1zzhb1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d1zzhb2
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d1zzhc1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d1zzhc2
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d1zzhd1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d1zzhd2
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	1zzhA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1zzhA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1zzhB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1zzhB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1zzhC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1zzhC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1zzhD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1zzhD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

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Unit-cell length a length_a	64.630 Å
Unit-cell length b length_b	132.470 Å
Unit-cell length c length_c	163.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2530
R_work r_work	0.2490
R_free r_free	0.2780