1cne

STRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE OF THE CYTOCHROME B REDUCTASE FRAGMENT AT 2.5 ANGSTROMS, ITS ADP COMPLEX AND AN ACTIVE SITE MUTANT AND MODELING OF THE CYTOCHROME B DOMAIN

Method: X-RAY DIFFRACTION D_max: 60.8 Å Quality: EXCELLENT

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

NITRATE REDUCTASE

Zea mays

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 352–621	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1CNE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CNF STRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE OF THE CYTOCHROME B REDUCTASE FRAGMENT AT 2.5 ANGSTROMS, ITS ADP COMPLEX AND AN ACTIVE SITE MUTANT AND MODELING OF THE CYTOCHROME B DOMAIN Deposited 1995-02-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 352–621（270 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å R-free 0.272
2CND STRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE OF THE CYTOCHROME B REDUCTASE FRAGMENT AT 2.5 ANGSTROMS, ITS ADP COMPLEX AND AN ACTIVE SITE MUTANT AND MODELING OF THE CYTOCHROME B DOMAIN Deposited 1995-02-01	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 352–621（270 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.223

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NIA1_MAIZE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–270； UniProt 352–621

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cne
Deposition date deposition_date	1995-02-01
Structure title title	STRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE OF THE CYTOCHROME B REDUCTASE FRAGMENT AT 2.5 ANGSTROMS, ITS ADP COMPLEX AND AN ACTIVE SITE MUTANT AND MODELING OF THE CYTOCHROME B DOMAIN
Keywords keywords	OXIDOREDUCTASE, NITROGENOUS ACCEPTOR, NITRATE ASSIMILATING ENZYME; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.90 Å
Radius of gyration Rg (electron density) rg_electron	18.62 Å
Forward intensity I(0) i0	16166300.00
Molecular weight molecular_weight	30255.0 kDa
Excluded volume excluded_volume	37857 Å³
Envelope volume envelope_volume	44370 Å³
Hydration-shell volume shell_volume	19744 Å³
Envelope diameter envelope_diameter	60.5 Å
Shell Rg shell_rg	24.97 Å
Envelope Rg envelope_rg	18.74 Å
Shape Rg shape_rg	18.62 Å
Total Rg total_rg	19.51 Å
Total atoms total_atoms	2127
Residues n_residues	260
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	60.8 Å
Rg (real space) rg_real	19.74 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.6170e+07
I(0) uncertainty (real space) i0_real_error	2.0530e+05
Rg (reciprocal space) rg_reciprocal	19.77 Å
I(0) (reciprocal space) i0_reciprocal	16170000.0000
Solution quality estimate total_estimate	0.9061
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	59.9 Å
Skewness Skewness skewness	0.090
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3082000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cnea1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.2 — Ferredoxin reductase FAD-binding domain-like

Domain ID domain_id	d1cnea2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.1 — Reductases

CATH v4.4 (2 domains)

Domain ID domain_id	1cneA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	1cneA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

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8. Citations (4)

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Unit-cell length a length_a	145.200 Å
Unit-cell length b length_b	145.200 Å
Unit-cell length c length_c	47.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1900
R_work r_work	0.1900
R_free r_free	—

Description description	NITRATE REDUCTASE
Molecular weight formula_weight	30574.3 kDa
EC 编号 ec_number	1.6.6.1
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2127

STRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE OF THE CYTOCHROME B REDUCTASE FRAGMENT AT 2.5 ANGSTROMS, ITS ADP COMPLEX AND AN ACTIVE SITE MUTANT AND MODELING OF THE CYTOCHROME B DOMAIN

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

NITRATE REDUCTASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Zea mays
NCBI Class编号 ncbi_taxonomy_id	4577

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/cn/1cne/1cne.fit
pddf	/app/data/pr_computation/cn/1cne/1cne.pr.out
profile	/app/data/saxs_computation/cn/1cne/1cne.dat