5guw

Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa

Method: X-RAY DIFFRACTION

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

Nitric oxide reductase subunit C

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nitric oxide reductase subunit B × 1 （Q59647） HEME C × 1 CALCIUM ION × 1 decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 1 PROTOPORPHYRIN IX CONTAINING FE × 2 FE (III) ION × 1 OXYGEN ATOM × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Nitric oxide reductase subunit B × 1 （Q59647） HEME C × 1 CALCIUM ION × 1 decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 FE (III) ION × 1 OXYGEN ATOM × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NORC_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–146； UniProt 1–146 Author chain C； PDBConstruct 1–146； UniProt 1–146

Nitric oxide reductase subunit B

OrganismNot specified

UniProt Q59647

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nitric oxide reductase subunit C × 1 （Q59646） HEME C × 1 CALCIUM ION × 1 decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 1 PROTOPORPHYRIN IX CONTAINING FE × 2 FE (III) ION × 1 OXYGEN ATOM × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Nitric oxide reductase subunit C × 1 （Q59646） HEME C × 1 CALCIUM ION × 1 decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 FE (III) ION × 1 OXYGEN ATOM × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NORB_PSEAE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–465； UniProt 1–466 Author chain D； PDBConstruct 1–465； UniProt 1–466

Nitrite reductase

OrganismNot specified

UniProt P24474

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
3	Protein homooligomer	Homooligomer	Protein 2	HEME C × 2 HEME D × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIRS_PSEAE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–568； UniProt 1–568 Author chain N； PDBConstruct 1–568； UniProt 1–568

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	5guw
Deposition date deposition_date	2016-08-31
Structure title title	Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa
Keywords keywords	metal-binding, membrane protein; MEMBRANE PROTEIN
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.

5guw__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5guw__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5guw__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.96 Å
Rg (electron density)	23.73 Å
Total Rg	24.80 Å
Atom count	4897
Residues	591
Excluded volume	89443 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5guw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5guw__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5guw__assembly_3__model_1`	dimeric （2）	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 (12)

Entity 1 Entity 1 polymer

Description description	Nitric oxide reductase subunit C
Molecular weight formula_weight	16374.6 kDa
Mutation mutation	K100N
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	18387

MSETFTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMKIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG

Entity 2 Entity 2 polymer

Description description	Nitric oxide reductase subunit B
Molecular weight formula_weight	52215.9 kDa
EC 编号 ec_number	1.7.2.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MMSPNGSLKFASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRRDYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSFRRGKAAA

Entity 3 Entity 3 polymer

Description description	Nitrite reductase
Molecular weight formula_weight	62736.1 kDa
EC 编号 ec_number	1.7.2.1,1.7.99.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N

MPFGKPLVGTLLASLTLLGLATAHAKDDMKAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY

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	4

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside
Molecular weight formula_weight	498.6 kDa
Source method src_method	man
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	OXYGEN ATOM
Molecular weight formula_weight	16.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	HEME D
Molecular weight formula_weight	712.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5guwA00
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	5guwB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

Domain ID domain_id	5guwC00
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	5guwD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

Domain ID domain_id	5guwM01
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	5guwM02
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	20 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

Domain ID domain_id	5guwN01
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	5guwN02
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	20 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

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Unit-cell length a length_a	111.871 Å
Unit-cell length b length_b	128.606 Å
Unit-cell length c length_c	127.807 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	49.480 Å
R factor r_factor	0.2119
R_work r_work	0.2097
R_free r_free	0.2540

Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa

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

Nitric oxide reductase subunit C

State in the Current Structure

Other States of the Same Protein in the Database

Nitric oxide reductase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Nitrite reductase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5guw__assembly_2__model_1

5guw__assembly_2__model_1 | I(q)

5guw__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (4)

Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa

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

Nitric oxide reductase subunit C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitric oxide reductase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitrite reductase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5guw__assembly_2__model_1

5guw__assembly_2__model_1 | I(q)

5guw__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (4)