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6tsi

cd1 nitrite reductase NirS with bound dihydro-heme d1

Method: X-RAY DIFFRACTION Dmax: 108.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nitrite reductase

OrganismNot specified

UniProt P24474

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 26–568 Chain B； UniProt 26–568 Not recorded HEC HEME C × 2 DHE HEME D × 2 PO4 PHOSPHATE ION × 5 CL CHLORIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.9M K2HPO4 0.1M Tris-HCl pH 8 Resolution 2.38 Å R-free 0.280

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 6TSI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BL9 CONFORMATIONAL CHANGES OCCURRING UPON REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-07-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Chain B 26–568（543 aa）
Not recorded HEC HEME C × 2 DHE HEME D × 2 OH HYDROXIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 2.90 Å R-free 0.233
1GJQ Pseudomonas aeruginosa cd1 nitrite reductase reduced cyanide complex Deposited 2001-08-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Chain B 26–568（543 aa）
Not recorded HEC HEME C × 2 DHE HEME D × 2 CYN CYANIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；2M NA/K2 PHOSPHATE, 50MM TRIS-HCL, PH 8.4
Resolution 2.70 Å R-free 0.247
1HZU DOMAIN SWING UPON HIS TO ALA MUTATION IN NITRITE REDUCTASE OF PSEUDOMONAS AERUGINOSA Deposited 2001-01-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Mutation：H327A HEC HEME C × 2 DHE HEME D × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；PEG 5000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.248
1HZV DOMAIN SWING UPON HIS TO ALA MUTATION IN NITRITE REDUCTASE OF PSEUDOMONAS AERUGINOSA Deposited 2001-01-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Mutation：H369A HEC HEME C × 2 DHE HEME D × 2 NO NITRIC OXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.83 Å R-free 0.296
1N15 FOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-09-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Chain B 26–568（543 aa）
Not recorded HEC HEME C × 2 DHE HEME D × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 2.90 Å R-free 0.247
1N50 FOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-09-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Chain B 26–568（543 aa）
Not recorded HEC HEME C × 2 DHE HEME D × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 2.90 Å R-free 0.246
1N90 FOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-09-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Chain B 26–568（543 aa）
Not recorded HEC HEME C × 2 DHE HEME D × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 2.90 Å R-free 0.241
1NIR OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1997-06-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Chain B 26–568（543 aa）
Not recorded PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 2 OH HYDROXIDE ION × 2 HEC HEME C × 2 DHE HEME D × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.4；PROTEIN WAS CRYSTALLIZED FROM @M NA/K2 PHOSPHATE, 50MM TRIS-HCL, PH 8.4
Resolution 2.15 Å R-free 0.242
1NNO CONFORMATIONAL CHANGES OCCURRING UPON NO BINDING IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-07-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Chain B 26–568（543 aa）
Not recorded HEC HEME C × 2 DHE HEME D × 2 NO NITRIC OXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 2.65 Å R-free 0.243
5GUW Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa Deposited 2016-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain M 1–568（568 aa） Fragment：cd1 nitrite reductase
Chain N 1–568（568 aa） Fragment：cd1 nitrite reductase
Not recorded HEC HEME C × 2 DHE HEME D × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, 0.2M CsCl, 12% PEG3350
Resolution 3.20 Å R-free 0.254
6TPO Conformation of cd1 nitrite reductase NirS without bound heme d1 Deposited 2019-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–568（543 aa）
Not recorded 1PE PENTAETHYLENE GLYCOL × 2 BU3 (R,R)-2,3-BUTANEDIOL × 2 HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.1M Phosphate/citrate pH4.2 40% (v/v) PEG300
Resolution 1.86 Å R-free 0.194

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NIRS_PSEAE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–543； UniProt 26–568 Author chain B； PDBConstruct 1–543； UniProt 26–568

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6tsi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6tsi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6tsi
Deposition date deposition_date2019-12-20
Structure title titlecd1 nitrite reductase NirS with bound dihydro-heme d1
Keywords keywordscd1 nitrite reductase, NirS, OXIDOREDUCTASE; 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_guinier32.98 Å
Radius of gyration Rg (electron density) rg_electron32.48 Å
Forward intensity I(0) i0232861000.00
Molecular weight molecular_weight121770.0 kDa
Excluded volume excluded_volume151810 ų
Envelope volume envelope_volume180180 ų
Hydration-shell volume shell_volume45842 ų
Envelope diameter envelope_diameter113.9 Å
Shell Rg shell_rg39.67 Å
Envelope Rg envelope_rg32.56 Å
Shape Rg shape_rg32.48 Å
Total Rg total_rg32.97 Å
Total atoms total_atoms16870
Residues n_residues1080
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 dmax108.2 Å
Rg (real space) rg_real32.99 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real2.3290e+08
I(0) uncertainty (real space) i0_real_error3.4530e+06
Rg (reciprocal space) rg_reciprocal32.99 Å
I(0) (reciprocal space) i0_reciprocal232900000.0000
Solution quality estimate total_estimate0.8858
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.0 Å
Skewness Skewness skewness0.357
Kurtosis Kurtosis kurtosis-0.417
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha74160000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.883
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6tsia1
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.2 — N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
Domain ID domain_idd6tsia2
Class classb — All beta proteins
Fold Fold foldb.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamilyb.70.2 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
Family Family familyb.70.2.1 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
Domain ID domain_idd6tsib1
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.2 — N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
Domain ID domain_idd6tsib2
Class classb — All beta proteins
Fold Fold foldb.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamilyb.70.2 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
Family Family familyb.70.2.1 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
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8. Citations (1)

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9. Files and Curves (10)