1cp2

NITROGENASE IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM

Method: X-RAY DIFFRACTION Dmax: 74.8 Å Quality: EXCELLENT

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

NITROGENASE IRON PROTEIN

OrganismNot specified

UniProt P00456

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–269 Chain B; UniProt 1–269 Not recorded SF4 IRON/SULFUR CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:liquid - liquid diffusion;pH 7.5;PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD. PRECIPITANT CONTAINED 5-15% GLYCEROL, 18.75-22.5% PEG 4000, 230-270 MM CACL2, AND 50 MM HEPES PH 7.5. PROTEIN WAS STORED BEFORE CRYSTALLIZATION IN 20% GLYCEROL, 50 MM HEPES, PH 7.5, AND 2 MM NA2S2O4., liquid - liquid diffusion Resolution 1.93 Å R-free 0.297

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name NIFH1_CLOPA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–269; UniProt 1–269 Author chain B; PDBConstruct 1–269; UniProt 1–269

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 1cp2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1cp2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1cp2
Deposition date deposition_date1998-05-11
Structure title titleNITROGENASE IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM
Keywords keywordsOXIDOREDUCTASE, NITROGENASE IRON PROTEIN; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.51
Radius of gyration Rg (electron density) rg_electron23.37
Forward intensity I(0) i058411900.00
Molecular weight molecular_weight58713.0 kDa
Excluded volume excluded_volume73157 ų
Envelope volume envelope_volume85062 ų
Hydration-shell volume shell_volume29654 ų
Envelope diameter envelope_diameter77.0
Shell Rg shell_rg30.98
Envelope Rg envelope_rg23.24
Shape Rg shape_rg23.41
Total Rg total_rg24.04
Total atoms total_atoms4088
Residues n_residues538
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax74.8
Rg (real space) rg_real24.36
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real5.8410e+07
I(0) uncertainty (real space) i0_real_error7.2630e+05
Rg (reciprocal space) rg_reciprocal24.40
I(0) (reciprocal space) i0_reciprocal58410000.0000
Solution quality estimate total_estimate0.9085
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.9
Skewness Skewness skewness0.173
Kurtosis Kurtosis kurtosis-0.476
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10850000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1cp2a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.10 — Nitrogenase iron protein-like
Domain ID domain_idd1cp2b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.10 — Nitrogenase iron protein-like

CATH v4.4 (2 domains)

Domain ID domain_id1cp2A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1cp2B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)