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2zzs

Crystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c554

Vibrio parahaemolyticus

UniProt Q87MF5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
10 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
11 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
12 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
13 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
14 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
15 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
16 Protein monomer Monomer Protein 1 HEME C × 1 GLYCEROL × 1 water × 1 Consistent with protein count
17 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
18 Protein monomer Monomer Protein 1 HEME C × 1 GLYCEROL × 1 water × 1 Consistent with protein count
19 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
20 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
21 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
22 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
23 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
24 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
25 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
26 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
27 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
28 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
29 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 HEME C × 1 GLYCEROL × 1 water × 1 Consistent with protein count
30 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
31 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
32 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 HEME C × 1 GLYCEROL × 1 water × 1 Consistent with protein count
6 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
7 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
8 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count
9 Protein monomer Monomer Protein 1 HEME C × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2zzs 2zzs 2zzs 2zzs 2zzs 2zzs 2zzs 2zzs 2zzs 2zzs 2zzs 2zzs

32 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name Q87MF5_VIBPA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain 1； PDBConstruct 1–103； UniProt 1–103 Author chain 2； PDBConstruct 1–103； UniProt 1–103 Author chain 3； PDBConstruct 1–103； UniProt 1–103 Author chain 4； PDBConstruct 1–103； UniProt 1–103 Author chain 5； PDBConstruct 1–103； UniProt 1–103 Author chain 6； PDBConstruct 1–103； UniProt 1–103 Author chain A； PDBConstruct 1–103； UniProt 1–103 Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain C； PDBConstruct 1–103； UniProt 1–103 Author chain D； PDBConstruct 1–103； UniProt 1–103 Author chain E； PDBConstruct 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103 Author chain G； PDBConstruct 1–103； UniProt 1–103 Author chain H； PDBConstruct 1–103； UniProt 1–103 Author chain I； PDBConstruct 1–103； UniProt 1–103 Author chain J； PDBConstruct 1–103； UniProt 1–103 Author chain K； PDBConstruct 1–103； UniProt 1–103 Author chain L； PDBConstruct 1–103； UniProt 1–103 Author chain M； PDBConstruct 1–103； UniProt 1–103 Author chain N； PDBConstruct 1–103； UniProt 1–103 Author chain O； PDBConstruct 1–103； UniProt 1–103 Author chain P； PDBConstruct 1–103； UniProt 1–103 Author chain Q； PDBConstruct 1–103； UniProt 1–103 Author chain R； PDBConstruct 1–103； UniProt 1–103 Author chain S； PDBConstruct 1–103； UniProt 1–103 Author chain T； PDBConstruct 1–103； UniProt 1–103 Author chain U； PDBConstruct 1–103； UniProt 1–103 Author chain V； PDBConstruct 1–103； UniProt 1–103 Author chain W； PDBConstruct 1–103； UniProt 1–103 Author chain X； PDBConstruct 1–103； UniProt 1–103 Author chain Y； PDBConstruct 1–103； UniProt 1–103 Author chain Z； PDBConstruct 1–103； UniProt 1–103

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_id2zzs
Deposition date deposition_date2009-02-24
Structure title titleCrystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633
Keywords keywordsc-type cytochrome, cytochrome c554, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method methodX-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.

2zzs__assembly_18__model_1

Assembly 18 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2zzs__assembly_18__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2zzs__assembly_18__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）12.62 Å
Rg (electron density)11.25 Å
Total Rg12.62 Å
Atom count624
Residues81
Excluded volume11014 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2zzs__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2zzs__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2zzs__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 2zzs__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 2zzs__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 2zzs__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 2zzs__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 2zzs__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 2zzs__assembly_9__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 2zzs__assembly_10__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
11 1 2zzs__assembly_11__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
12 1 2zzs__assembly_12__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
13 1 2zzs__assembly_13__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
14 1 2zzs__assembly_14__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
15 1 2zzs__assembly_15__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
16 1 2zzs__assembly_16__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
17 1 2zzs__assembly_17__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
18 1 2zzs__assembly_18__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
19 1 2zzs__assembly_19__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
20 1 2zzs__assembly_20__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
21 1 2zzs__assembly_21__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
22 1 2zzs__assembly_22__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
23 1 2zzs__assembly_23__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
24 1 2zzs__assembly_24__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
25 1 2zzs__assembly_25__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
26 1 2zzs__assembly_26__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
27 1 2zzs__assembly_27__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
28 1 2zzs__assembly_28__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
29 1 2zzs__assembly_29__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
30 1 2zzs__assembly_30__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
31 1 2zzs__assembly_31__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
32 1 2zzs__assembly_32__model_1 monomeric （1） 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 (4)

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6. Fold Classification (SCOP + CATH) 32 domains

CATH v4.4 (32 domains)

Domain ID domain_id2zzs100
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzs200
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzs300
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzs400
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzs500
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzs600
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsI00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsJ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsK00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsL00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsM00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsN00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsO00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsP00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsQ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsR00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsS00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsT00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsU00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsV00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsW00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsX00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsY00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2zzsZ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
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7. Citations (1)