1ogy

Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides

Method: X-RAY DIFFRACTION

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

PERIPLASMIC NITRATE REDUCTASE

RHODOBACTER SPHAEROIDES

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE × 1 （Q53177） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE × 1 （Q53177） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE × 1 （Q53177） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE × 1 （Q53177） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE × 1 （Q53177） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE × 1 （Q53177） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE × 1 （Q53177） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE × 1 （Q53177） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAPA_RHOSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–802； UniProt 30–831 Author chain C； PDBConstruct 1–802； UniProt 30–831 Author chain E； PDBConstruct 1–802； UniProt 30–831 Author chain G； PDBConstruct 1–802； UniProt 30–831 Author chain I； PDBConstruct 1–802； UniProt 30–831 Author chain K； PDBConstruct 1–802； UniProt 30–831 Author chain M； PDBConstruct 1–802； UniProt 30–831 Author chain O； PDBConstruct 1–802； UniProt 30–831

DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE

RHODOBACTER SPHAEROIDES

UniProt Q53177

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PERIPLASMIC NITRATE REDUCTASE × 1 （Q53176） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PERIPLASMIC NITRATE REDUCTASE × 1 （Q53176） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	PERIPLASMIC NITRATE REDUCTASE × 1 （Q53176） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	PERIPLASMIC NITRATE REDUCTASE × 1 （Q53176） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	PERIPLASMIC NITRATE REDUCTASE × 1 （Q53176） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	PERIPLASMIC NITRATE REDUCTASE × 1 （Q53176） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	PERIPLASMIC NITRATE REDUCTASE × 1 （Q53176） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	PERIPLASMIC NITRATE REDUCTASE × 1 （Q53176） IRON/SULFUR CLUSTER × 1 MOLYBDENUM ATOM × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 HEME C × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAPB_RHOSH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–130； UniProt 25–154 Author chain D； PDBConstruct 1–130； UniProt 25–154 Author chain F； PDBConstruct 1–130； UniProt 25–154 Author chain H； PDBConstruct 1–130； UniProt 25–154 Author chain J； PDBConstruct 1–130； UniProt 25–154 Author chain L； PDBConstruct 1–130； UniProt 25–154 Author chain N； PDBConstruct 1–130； UniProt 25–154 Author chain P； PDBConstruct 1–130； UniProt 25–154

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	1ogy
Deposition date deposition_date	2003-05-19
Structure title title	Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides
Keywords keywords	NITRATE REDUCTASE, 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.

1ogy__assembly_1__model_1

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

Download this curve (.dat)

1ogy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ogy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.28 Å
Rg (electron density)	26.36 Å
Total Rg	27.11 Å
Atom count	7417
Residues	917
Excluded volume	130190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ogy__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ogy__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1ogy__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1ogy__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1ogy__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1ogy__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1ogy__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`1ogy__assembly_8__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 (6)

Entity 1 Entity 1 polymer

Description description	PERIPLASMIC NITRATE REDUCTASE
Molecular weight formula_weight	90114.6 kDa
EC 编号 ec_number	1.7.99.4
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	59336

QPVTGGAEALRIRWSKAPCRFCGTGCGVMVGTRDGQVVATHGDTQAEVNRGLNCVKGYFLSKIMYGEDRLTTPLLRMKDGVYHKEGEFAPVSWDEAFDVMAAQAKLVLKEKAPEAVGMFGSGQWTIWEGYAASKLMRAGFRSNNLDPNARHCMASAATAFMRTFGMDEPMGCYDDFEAADAFVLWGSNMAEMHPILWSRLTDRRLSHEHVRVAVLSTFTHRSSDLSDTPIIFRPGTDRAILNYIAHHIISTGRVNRDFVDRHTNFALGATDIGYGLRPEHQLQLAAKGAADAGAMTPTDFETFAALVSEYTLEKAAEISGVEPALLEELAELYADPDRKWMSLWTMGFNQHVRGVWANHMVYNLHLLTGKISEPGNSPFSLTGQPFACGTAREVGTFAHRLPADMVVTNPEHRAHAEEIWKLPAGLLPDWVGAHAVEQDRKLHDGEINFYWVQVNNNMQAAPNIDQETYPGYRNPENFIVVSDAYPTVTGRAADLVLPAAMWVEKEGAYGNAERRTHFWHQLVEAPGEARSDLWQLMEFSKRFTTDEVWPEEILSAAPAYRGKTLFEVLFANGSVDRFPASDVNPDHANHEAALFGFYPQKGLFEEYAAFGRGHGHDLAPFDTYHEVRGLHWPVVEGEETRWRYREGFDPYVKPGEGLRFYGKPDGRAVILGVPYEPPAESPDEEFGFWLVTGRVLEHWHSGSMTLRWPELYKAFPGAVCFMHPEDARSRGLNRGSEVRVISRRGEIRTRLETRGRNRMPRGVVFVPWFDASQLINKVTLDANDPISRQTDFKKCAVKIEAV

Source Source

Source organism organism	RHODOBACTER SPHAEROIDES
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	RHODOBACTER SPHAEROIDES

Entity 2 Entity 2 polymer

Description description	DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
Molecular weight formula_weight	14590.4 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P

QDAPRLTGADRPMSEVAAPPLPETITDDRRVGRNYPEQPPVIPHSIEGYQLSVNANRCLECHRRQYSGLVAAPMISITHFQDREGQMLADVSPRRYFCTACHVPQTNAQPLVTNEFRDMLTLMPASNEAE

Source Source

Source organism organism	RHODOBACTER SPHAEROIDES
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	RHODOBACTER SPHAEROIDES

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	MOLYBDENUM ATOM
Molecular weight formula_weight	95.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
Molecular weight formula_weight	740.6 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 6 Entity 6 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 56 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d1ogya1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

Domain ID domain_id	d1ogya2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d1ogyb_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1ogyc1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

Domain ID domain_id	d1ogyc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d1ogyd_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1ogye1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

Domain ID domain_id	d1ogye2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d1ogyf_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1ogyg1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

Domain ID domain_id	d1ogyg2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d1ogyh_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1ogyi1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

Domain ID domain_id	d1ogyi2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d1ogyj_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1ogyk1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

Domain ID domain_id	d1ogyk2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d1ogyl_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1ogym1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

Domain ID domain_id	d1ogym2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d1ogyn_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1ogyo1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

Domain ID domain_id	d1ogyo2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d1ogyp_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

CATH v4.4 (32 domains)

Domain ID domain_id	1ogyA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	1ogyA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	1ogyA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	1ogyA04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ogyC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	1ogyC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	1ogyC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	1ogyC04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ogyE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	1ogyE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	1ogyE03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	1ogyE04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ogyG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	1ogyG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	1ogyG03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	1ogyG04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ogyI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	1ogyI02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	1ogyI03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	1ogyI04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ogyK01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	1ogyK02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	1ogyK03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	1ogyK04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ogyM01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	1ogyM02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	1ogyM03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	1ogyM04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ogyO01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	1ogyO02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	1ogyO03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	1ogyO04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	123.000 Å
Unit-cell length b length_b	225.200 Å
Unit-cell length c length_c	154.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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	30.000 Å
R factor r_factor	0.2504
R_work r_work	0.2504
R_free r_free	0.2687

Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides

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

PERIPLASMIC NITRATE REDUCTASE

State in the Current Structure

Other States of the Same Protein in the Database

DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE 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

1ogy__assembly_1__model_1

1ogy__assembly_1__model_1 | I(q)

1ogy__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 56 domains

SCOP 2.08 (24 domains)

CATH v4.4 (32 domains)

7. Citations (3)

Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides

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

PERIPLASMIC NITRATE 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

DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE 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

1ogy__assembly_1__model_1

1ogy__assembly_1__model_1 | I(q)

1ogy__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 56 domains

SCOP 2.08 (24 domains)

CATH v4.4 (32 domains)

7. Citations (3)