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1k3h

NMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii

Method: SOLUTION NMR Dmax: 36.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

cytochrome c-553

Sporosarcina pasteurii

UniProt P82599

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 22–92 Fragment：RESIDUES 22-92 HEC HEME C × 1 SOLUTION NMR NMR measurement conditions：pH 7.5；288 K；Ionic strength (raw mmCIF value) 10 mM phosphate buffer；Pressure Ambient NMR sample composition：1-3 mM oxidized cytochrome c-553 in 10 mM phosphate buffer | 90%H2O+10%D2O; 100% D2O Resolution not provided

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 1K3H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B7V Structure of the C-553 cytochrome from Bacillus pasteruii to 1.7 A resolution Deposited 1999-01-22 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–92（71 aa）
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；8MG/ML OF CYTOCHROME, 20MM TRIS.HCL, PH 8.0 AT 20 DEGREES C, HANGING DROPS IN HAMPTON RESEARCH 24-WELL LINBRO PLATES, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.206
1C75 0.97 A "AB INITIO" CRYSTAL STRUCTURE OF CYTOCHROME C-553 FROM BACILLUS PASTEURII Deposited 2000-02-09 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–92（71 aa）
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；3.2 M AMMONIUM SULPHATE IN 100 MM SODIUM CITRATE BUFFER PH 5.0
Resolution 0.97 Å
1K3G NMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii Deposited 2001-10-03 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–92（71 aa） Fragment：residues 22-92
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 7.5；288 K；Ionic strength (raw mmCIF value) 10 mM phosphate buffer；Pressure Ambient
NMR sample composition 1-3 mM oxidized cytochrome c-553 in 10 mM phosphate buffer | 90%H2O+10%D2O; 100% D2O
Resolution not provided
1N9C Structure and dynamics of reduced Bacillus pasteurii cytochrome c: oxidation state dependent properties and implications for electron transfer processes Deposited 2002-11-23 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–92（71 aa） Fragment：soluble part of membrane-anchored cytochrome c
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 100 mM Pi；Pressure ambient
NMR sample composition 2 mM cytochrome, 100mM phosphate buffer, pH 7.0 | 90% H2O/10% D2O
NMR sample composition 1 mM cytochrome U-15N, 100mM phosphate buffer, pH 7.0 | 90% H2O/10% D2O
Resolution not provided

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CY553_BACPA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–71； UniProt 22–92

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 1k3h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1k3h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1k3h
Deposition date deposition_date2001-10-03
Structure title titleNMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii
Keywords keywordsC-553, HEME, CYTOCHROME, BACILLUS PASTEURII, electron transfer, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.00 Å
Radius of gyration Rg (electron density) rg_electron10.42 Å
Forward intensity I(0) i01356500.00
Molecular weight molecular_weight7722.0 kDa
Excluded volume excluded_volume9587 ų
Envelope volume envelope_volume9950 ų
Hydration-shell volume shell_volume8179 ų
Envelope diameter envelope_diameter32.5 Å
Shell Rg shell_rg15.99 Å
Envelope Rg envelope_rg10.80 Å
Shape Rg shape_rg10.42 Å
Total Rg total_rg11.85 Å
Total atoms total_atoms1058
Residues n_residues71
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 dmax36.7 Å
Rg (real space) rg_real11.89 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real1.3570e+06
I(0) uncertainty (real space) i0_real_error1.4610e+04
Rg (reciprocal space) rg_reciprocal11.90 Å
I(0) (reciprocal space) i0_reciprocal1357000.0000
Solution quality estimate total_estimate0.8854
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary16.7 Å
Skewness Skewness skewness0.010
Kurtosis Kurtosis kurtosis-0.333
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha340500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.850; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.986
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1k3ha_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.1 — monodomain cytochrome c

CATH v4.4 (1 domains)

Domain ID domain_id1k3hA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
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8. Citations (3)

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9. Files and Curves (10)