SAXSdb — 1ib7

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

CYTOCHROME B5

Rattus rattus

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 5–98	Mutation：F35Y	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions：pH 7；313 K；Ionic strength (raw mmCIF value) 1mM NMR measurement conditions：pH 7；313 K；Ionic strength (raw mmCIF value) 1mM NMR measurement conditions：pH 7；313 K；Ionic strength (raw mmCIF value) 1mM NMR sample composition：2mM F35Y CYTOCHROME B5; 1mM PHOSPHATE BUFFER; PURGED WITH NITROGEN GAS AND REDUCED BY ADDING FEW GRAINS OF SODIUM DITHIONATE AND SEALED USING OXY-ACETYLENE TORCH; 0.05 mM TSP AS INTERNAL REFERENCE \| 90% H2O/10% D2O NMR sample composition：2mM F35Y CYTOCHROME B5; 1mM PHOSPHATE BUFFER; PURGED WITH NITROGEN GAS AND REDUCED BY ADDING FEW GRAINS OF SODIUM DITHIONATE AND SEALED USING OXY-ACETYLENE TORCH; 0.05 mM TSP AS INTERNAL REFERENCE \| 90% H2O/10% D2O NMR sample composition：2mM F35Y CYTOCHROME B5; 1mM PHOSPHATE BUFFER; PURGED WITH NITROGEN GAS AND REDUCED BY ADDING FEW GRAINS OF SODIUM DITHIONATE AND SEALED USING OXY-ACETYLENE TORCH; 0.05 mM TSP AS INTERNAL REFERENCE \| 90% H2O/10% 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 1IB7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AQA SOLUTION STRUCTURE OF REDUCED MICROSOMAL RAT CYTOCHROME B5, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-07-28	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–98（94 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided
1AW3 THE SOLUTION NMR STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, MINIMIZED AVERAGE STRUCTURE Deposited 1997-10-09	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–98（94 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K	Resolution not provided
1AXX THE SOLUTION STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, NMR, 19 STRUCTURES Deposited 1997-10-22	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–98（94 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 1 mM PHOSPHATE；Pressure 1	Resolution not provided
1B5A RAT FERROCYTOCHROME B5 A CONFORMATION, NMR, 1 STRUCTURE Deposited 1998-04-06	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–98（94 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；313 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition [U-13C; U-15N] Cytochrome b5, 100 mM phosphate buffer, 0.5 mM TSP, pH 7.0, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
1B5B RAT FERROCYTOCHROME B5 B CONFORMATION, NMR, 1 STRUCTURE Deposited 1998-04-06	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–98（94 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；313 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition [U-13C; U-15N] Cytochrome b5, 100 mM phosphate buffer, 0.5 mM TSP, pH 7.0, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
1BFX THE SOLUTION NMR STRUCTURE OF THE B FORM OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, MINIMIZED AVERAGE STRUCTURE Deposited 1998-05-23	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) PHOSPHATE 1mM；Pressure 1 NMR sample composition H2O AND D2O	Resolution not provided
1BLV SOLUTION STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5 IN THE PRESENCE OF 2 M GUANIDINIUM CHLORIDE: MONITORING THE EARLY STEPS IN PROTEIN UNFOLDING Deposited 1998-07-21	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–98（94 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) PHOSPHATE BUFFER 100 mM PLUS 2 M GDMCL IN THE SAME BUFFER；Pressure 1	Resolution not provided
1I87 SOLUTION STRUCTURE OF THE WATER-SOLUBLE FRAGMENT OF RAT HEPATIC APOCYTOCHROME B5 Deposited 2001-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa） Fragment：WATER-SOLUBLE DOMAIN (RESIDUES 1-98)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K；Ionic strength (raw mmCIF value) low；Pressure ambient NMR sample composition 1 mM apocytochrome b5, 13C,15N \| 90% H2O/10% D2O NMR sample composition 1 mM apocytochrome b5, 15N \| 90% H2O/10% D2O NMR sample composition 2 mM apocytochrome b5 \| 90% H2O/10% D2O NMR sample composition 2 mM apocytochrome b5 \| 100% D2O	Resolution not provided
1I8C SOLUTION STRUCTURE OF THE WATER-SOLUBLE FRAGMENT OF RAT HEPATIC APOCYTOCHROME B5 Deposited 2001-03-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa） Fragment：WATER-SOLUBLE DOMAIN (RESIDUES 1-98)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K；Ionic strength (raw mmCIF value) low；Pressure ambient NMR sample composition 1 mM apocytochrome b5, 13C,15N \| 90% H2O/10% D2O NMR sample composition 1 mM apocytochrome b5, 15N \| 90% H2O/10% D2O NMR sample composition 2 mM apocytochrome b5 \| 90% H2O/10% D2O NMR sample composition 2 mM apocytochrome b5 \| 100% D2O	Resolution not provided
1IET APOCYTOCHROME B5, PH 6.2, 298 K, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-04-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K	Resolution not provided
1IEU APOCYTOCHROME B5, PH 6.2, 298 K, NMR, 10 STRUCTURES Deposited 1996-04-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K	Resolution not provided
1JEX SOLUTION STRUCTURE OF A67V MUTANT OF RAT FERRO CYTOCHROME B5 Deposited 2001-06-19	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–98（94 aa）	Mutation：A67V	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；313 K；Ionic strength (raw mmCIF value) 1 mM；Pressure ambient NMR sample composition 2MM F35Y CYTOCHROME B5;1MM PHOSPHATE BUFFER; PURGED WITH NITROGEN GAS AND REDUCED BY ADDING FEW GRAINS OF SODIUM DITHIONATE AND SEALED USING OXY-ACETYLENE TORCH; 0.05 MM TSP AS INTERNAL REFERENCE \| 90% H2O/10% D2O	Resolution not provided
1MNY Dimethyl propionate ester heme-containing cytochrome b5 Deposited 2002-09-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–98（94 aa） Fragment：soluble domain, RESIDUES 5-98	Not recorded	HDM DIMETHYL PROPIONATE ESTER HEME × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM potassium phosphate	Resolution not provided
2AXX THE SOLUTION STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, NMR, 21 STRUCTURES Deposited 1997-10-22	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–98（94 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) PHOSPHATE 1mM；Pressure 1	Resolution not provided
5XE4 NMR solution structure of the aromatic mutant H43W H67F cytochrome b5 Deposited 2017-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–99（98 aa） Fragment：UNP residues 2-99	Mutation：H43W, H63F, T77K	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；283 K；Ionic strength (raw mmCIF value) 60；Pressure 101 NMR sample composition 0.5 mM [U-99% 15N] WF cytochrome b5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N] WF cytochrome b5, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5XEE NMR solution structure of the aromatic mutant H43F H67F cytochrome b5 Deposited 2017-04-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–99（98 aa） Fragment：UNP residues 2-99	Mutation：H43F, H67F, T77K	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；283 K；Ionic strength (raw mmCIF value) 50；Pressure 101325 NMR sample composition 0.5 mM [U-99% 15N] FFcytb5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N] FFcytb5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] FFcytb5, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYB5_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 5–98

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ib7
Deposition date deposition_date	2001-03-27
Structure title title	SOLUTION STRUCTURE OF F35Y MUTANT OF RAT FERRO CYTOCHROME B5, A CONFORMATION, ENSEMBLE OF 20 STRUCTURES
Keywords keywords	CYTOCHROME B5, ELECTRON TRANSPORT, SOLUTION STRUCTURES; ELECTRON TRANSPORT
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.42 Å
Radius of gyration Rg (electron density) rg_electron	12.19 Å
Forward intensity I(0) i0	606330000.00
Molecular weight molecular_weight	207790.0 kDa
Excluded volume excluded_volume	258610 Å³
Envelope volume envelope_volume	19331 Å³
Hydration-shell volume shell_volume	12049 Å³
Envelope diameter envelope_diameter	43.5 Å
Shell Rg shell_rg	19.44 Å
Envelope Rg envelope_rg	13.91 Å
Shape Rg shape_rg	12.15 Å
Total Rg total_rg	12.45 Å
Total atoms total_atoms	28520
Residues n_residues	1700
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	42.5 Å
Rg (real space) rg_real	12.34 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	6.0630e+08
I(0) uncertainty (real space) i0_real_error	6.8630e+06
Rg (reciprocal space) rg_reciprocal	12.34 Å
I(0) (reciprocal space) i0_reciprocal	606300000.0000
Solution quality estimate total_estimate	0.8589
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.1 Å
Skewness Skewness skewness	0.119
Kurtosis Kurtosis kurtosis	-0.375
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	229600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.721; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999

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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_id	d1ib7a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
Superfamily Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
Family Family family	d.120.1.1 — Cytochrome b5

CATH v4.4 (1 domains)

Domain ID domain_id	1ib7A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	CYTOCHROME B5
Molecular weight formula_weight	10829.9 kDa
Mutation mutation	F35Y
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	28520

来源生物 organism	Rattus rattus
通用名 common_name	black rat
NCBI Class编号 ncbi_taxonomy_id	10117
宿主生物 host_organism	Escherichia coli

SOLUTION STRUCTURE OF F35Y MUTANT OF RAT FERRO CYTOCHROME B5, A CONFORMATION, ENSEMBLE OF 20 STRUCTURES

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

CYTOCHROME B5

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

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/ib/1ib7/1ib7.fit
pddf	/app/data/pr_computation/ib/1ib7/1ib7.pr.out
profile	/app/data/saxs_computation/ib/1ib7/1ib7.dat