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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

Method: X-RAY DIFFRACTION Dmax: 58.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NADH-DEPENDENT NITRATE REDUCTASE

Zea mays

UniProt P17571

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 2.50 Å R-free 0.223

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 2CND Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 3.00 Å
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

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

SAXS profile for 2cnd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2cnd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2cnd
Deposition date deposition_date1995-02-01
Structure title titleSTRUCTURAL 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 keywordsNITRATE ASSIMILATING ENZYME, OXIDOREDUCTASE, NITROGENOUS ACCEPTOR; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.83 Å
Radius of gyration Rg (electron density) rg_electron18.54 Å
Forward intensity I(0) i016238800.00
Molecular weight molecular_weight30271.0 kDa
Excluded volume excluded_volume37868 ų
Envelope volume envelope_volume43796 ų
Hydration-shell volume shell_volume19614 ų
Envelope diameter envelope_diameter59.5 Å
Shell Rg shell_rg24.86 Å
Envelope Rg envelope_rg18.62 Å
Shape Rg shape_rg18.55 Å
Total Rg total_rg19.43 Å
Total atoms total_atoms2127
Residues n_residues260
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.4 Å
Rg (real space) rg_real19.67 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real1.6240e+07
I(0) uncertainty (real space) i0_real_error2.1760e+05
Rg (reciprocal space) rg_reciprocal19.70 Å
I(0) (reciprocal space) i0_reciprocal16240000.0000
Solution quality estimate total_estimate0.8127
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks5
Primary peak position r_peak_primary21.4 Å
Skewness Skewness skewness0.074
Kurtosis Kurtosis kurtosis-0.542
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2727000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.819; Stabil: 0.903; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.405
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2cnda1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
Family Family familyb.43.4.2 — Ferredoxin reductase FAD-binding domain-like
Domain ID domain_idd2cnda2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family familyc.25.1.1 — Reductases

CATH v4.4 (2 domains)

Domain ID domain_id2cndA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id2cndA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
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8. Citations (4)

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9. Files and Curves (10)