SAXSdb — 1u9m

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

Cytochrome b5

Bos taurus

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 7–88	Fragment：trypsin-solubilized fragment Mutation：F58W	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；phosphate buffer, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.266
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 7–88	Fragment：trypsin-solubilized fragment Mutation：F58W	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；phosphate buffer, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.266
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 7–88	Fragment：trypsin-solubilized fragment Mutation：F58W	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；phosphate buffer, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.266
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 7–88	Fragment：trypsin-solubilized fragment Mutation：F58W	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；phosphate buffer, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.266
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 7–88	Fragment：trypsin-solubilized fragment Mutation：F58W	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；phosphate buffer, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.266
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 7–88	Fragment：trypsin-solubilized fragment Mutation：F58W	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；phosphate buffer, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.266

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 1U9M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CYO BOVINE CYTOCHROME B(5) Deposited 1994-08-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–97（93 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å
1EHB CRYSTAL STRUCTURE OF RECOMBINANT TRYPSIN-SOLUBILIZED FRAGMENT OF CYTOCHROME B5 Deposited 2000-02-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–89（82 aa） Fragment：TRYPSIN-SOLUBILIZED FRAGMENT	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；phosphate buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.248
1ES1 CRYSTAL STRUCTURE OF VAL61HIS MUTANT OF TRYPSIN-SOLUBILIZED FRAGMENT OF CYTOCHROME B5 Deposited 2000-04-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–89（82 aa） Fragment：TRYPSIN-SOLUBILIZED FRAGMENT	Mutation：VAL61HIS	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；phosphate buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.244
1F03 SOLUTION STRUCTURE OF OXIDIZED BOVINE MICROSOMAL CYTOCHROME B5 MUTANT (E44A, E48A, E56A, D60A) AND ITS INTERACTION WITH CYTOCHROME C Deposited 2000-05-14	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa）	Mutation：E44A, E48A, E56A, D60A	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1 NMR sample composition 6 mM cytochrome b5 mutant 1H \| 10 mM phosphate buffer, 90% H2O, 10% D2O NMR sample composition 6 mM cytochrome b5 mutant 1H \| 10 mM phosphate buffer, D2O	Resolution not provided
1F04 SOLUTION STRUCTURE OF OXIDIZED BOVINE MICROSOMAL CYTOCHROME B5 MUTANT (E44A, E48A, E56A, D60A) AND ITS INTERACTION WITH CYTOCHROME C Deposited 2000-05-14	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa）	Mutation：E44A, E48A, E56A, D60A	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1 NMR sample composition 6 mM cytochrome b5 mutant 1H \| 10 mM phosphate buffer , 90% H2O, 10% D2O NMR sample composition 6 mM cytochrome b5 mutant 1H \| 10 mM phosphate buffer, D2O	Resolution not provided
1HKO NMR structure of bovine cytochrome b5 Deposited 2003-03-10	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–104（104 aa） Fragment：HEME BINDING DOMAIN, RESIDUES 1-104	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；300 K	Resolution not provided
1I5U SOLUTION STRUCTURE OF CYTOCHROME B5 TRIPLE MUTANT (E48A/E56A/D60A) Deposited 2001-02-28	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–89（82 aa） Fragment：SOLUBLE DOMAIN (RESIDUES 8-89)	Mutation：E48A/E56A/D60A	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；303 K；Pressure 1 NMR measurement conditions pH 7；303 K；Pressure 1 NMR measurement conditions pH 7；303 K；Pressure 1 NMR measurement conditions pH 7；303 K；Pressure 1 NMR sample composition 4mM cytochrome b5 triple mutant(E48A/E56A/D60A) \| 90% H2O/10% D2O	Resolution not provided
1J0Q Solution Structure of Oxidized Bovine Microsomal Cytochrome b5 mutant V61H Deposited 2002-11-20	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：Trypsin-Solubilized Fragment	Mutation：V61H	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；293 K；Pressure ambient NMR sample composition 2.9mM enzyme, pH 7.0, 25mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
1LQX Crystal structure of V45E mutant of cytochrome b5 Deposited 2002-05-14	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：trypsin-solubilized fragment of cytochrome b5	Mutation：V45E	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；PHOSPHATE BUFFER, pH 7.5, VAPOR DIFFUSION, temperature 293.0K	Resolution 1.80 Å R-free 0.222
1LR6 Crystal structure of V45Y mutant of cytochrome b5 Deposited 2002-05-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：trypsin-solubilized fragment of cytochrome b5	Mutation：V45Y	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PHOSPHATE BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.236
1M20 Crystal Structure of F35Y Mutant of Trypsin-solubilized Fragment of Cytochrome b5 Deposited 2002-06-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：trypsin-solubilized fragment	Mutation：F35Y	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；phosphate buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.227
1M2I Crystal structure of E44A/E56A mutant of cytochrome b5 Deposited 2002-06-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：trypsin-solubilized fragment of cytochrome b5	Mutation：E44A, E56A	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PHOSPHATE BUFFER, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.80 Å R-free 0.232
1M2M Crystal structure of E44A/E48A/E56A/D60A mutant of cytochrome b5 Deposited 2002-06-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：trypsin-solubilized fragment of cytochrome b5	Mutation：E44A, E48A, E56A, D60A	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PHOSPHATE BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.238
1M59 Crystal Structure of P40V Mutant of Trypsin-solubilized Fragment of Cytochrome b5 Deposited 2002-07-09	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：trypsin-solubilized fragment	Mutation：P40V	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；phosphate buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.227
1NX7 Solution Structure of Oxidized Bovine Microsomal Cytochrome B5 Deposited 2003-02-10	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：RESIDUES 3-84	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 25mM Phosphate buffer；Pressure 1 NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 25mM Phosphate buffer；Pressure 1 NMR sample composition 3.0mM \| 90% H2O/10% D2O NMR sample composition 3.0mM \| 100% D2O	Resolution not provided
1SH4 Solution structure of oxidized bovine microsomal cytochrome B5 Mutant V45H Deposited 2004-02-25	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：residues 3-84	Mutation：V45H	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 25mM PHOSPHATE BUFFER；Pressure 1 NMR sample composition 3.0mM \| 90% H2O/10% D2O NMR sample composition 3.0mM \| 100% D2O	Resolution not provided
1U9U Crystal structure of F58Y mutant of cytochrome b5 Deposited 2004-08-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–88（82 aa） Fragment：Trypsin-solubilized fragment	Mutation：F58Y	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；phosphate buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.86 Å R-free 0.215
3OZZ Structure of a cytochrome b5 core-swap mutant Deposited 2010-09-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 8–89（82 aa） Fragment：N-TERMINAL HEME-BINDING DOMAIN (unp residues 8-89)	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；30% PEG8000, 0.2M MgAc, 0.1M Pipes, pH 7.0, VAPOR DIFFUSION, temperature 277K	Resolution 1.70 Å R-free 0.229
4HIN 2.4A Resolution Structure of Bovine Cytochrome b5 (S71L) Deposited 2012-10-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–89（82 aa）	Mutation：S71L	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；20% (w/v) PEG 8000, 100 mM Tris, 200 mM MgCl2, 10 mM CuCl2, pH 8.5, vapor diffusion, temperature 293K	Resolution 2.40 Å R-free 0.245
4HIN 2.4A Resolution Structure of Bovine Cytochrome b5 (S71L) Deposited 2012-10-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 8–89（82 aa）	Mutation：S71L	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；20% (w/v) PEG 8000, 100 mM Tris, 200 mM MgCl2, 10 mM CuCl2, pH 8.5, vapor diffusion, temperature 293K	Resolution 2.40 Å R-free 0.245
4HIN 2.4A Resolution Structure of Bovine Cytochrome b5 (S71L) Deposited 2012-10-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 8–89（82 aa）	Mutation：S71L	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；20% (w/v) PEG 8000, 100 mM Tris, 200 mM MgCl2, 10 mM CuCl2, pH 8.5, vapor diffusion, temperature 293K	Resolution 2.40 Å R-free 0.245
4HIN 2.4A Resolution Structure of Bovine Cytochrome b5 (S71L) Deposited 2012-10-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 8–89（82 aa）	Mutation：S71L	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；20% (w/v) PEG 8000, 100 mM Tris, 200 mM MgCl2, 10 mM CuCl2, pH 8.5, vapor diffusion, temperature 293K	Resolution 2.40 Å R-free 0.245

19 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYB5_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–82； UniProt 7–88 Author chain B； PDBConstruct 1–82； UniProt 7–88 Author chain C； PDBConstruct 1–82； UniProt 7–88 Author chain D； PDBConstruct 1–82； UniProt 7–88 Author chain E； PDBConstruct 1–82； UniProt 7–88 Author chain F； PDBConstruct 1–82； UniProt 7–88

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	1u9m
Deposition date deposition_date	2004-08-10
Structure title title	Crystal structure of F58W mutant of cytochrome b5
Keywords keywords	;hemoprotein, F58Y and F58W mutants, conformational changes, aromatic-aromatic interactions, structure-function relationship, ELECTRON TRANSPORT ;; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	31.39 Å
Radius of gyration Rg (electron density) rg_electron	31.05 Å
Forward intensity I(0) i0	60225200.00
Molecular weight molecular_weight	60653.0 kDa
Excluded volume excluded_volume	75365 Å³
Envelope volume envelope_volume	100270 Å³
Hydration-shell volume shell_volume	29413 Å³
Envelope diameter envelope_diameter	113.0 Å
Shell Rg shell_rg	34.75 Å
Envelope Rg envelope_rg	31.22 Å
Shape Rg shape_rg	31.05 Å
Total Rg total_rg	31.41 Å
Total atoms total_atoms	4296
Residues n_residues	492
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	109.1 Å
Rg (real space) rg_real	31.63 Å
Rg uncertainty (real space) rg_real_error	1.47 Å
I(0) (real space) i0_real	6.0230e+07
I(0) uncertainty (real space) i0_real_error	1.0690e+06
Rg (reciprocal space) rg_reciprocal	31.53 Å
I(0) (reciprocal space) i0_reciprocal	60220000.0000
Solution quality estimate total_estimate	0.8535
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.7 Å
Skewness Skewness skewness	0.488
Kurtosis Kurtosis kurtosis	-0.274
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4897000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.831

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cytochrome b5
Molecular weight formula_weight	9514.4 kDa
Mutation mutation	F58W
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	4488

AVKYYTLEEIQKHNNSKSTWLILHYKVYDLTKFLEEHPGGEEVLREQAGGDATENWEDVGHSTDARELSKTFIIGELHPDDR

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	150

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1u9ma_
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

Domain ID domain_id	d1u9mb_
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

Domain ID domain_id	d1u9mc_
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

Domain ID domain_id	d1u9md_
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

Domain ID domain_id	d1u9me_
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

Domain ID domain_id	d1u9mf_
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 (6 domains)

Domain ID domain_id	1u9mA00
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

Domain ID domain_id	1u9mB00
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

Domain ID domain_id	1u9mC00
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

Domain ID domain_id	1u9mD00
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

Domain ID domain_id	1u9mE00
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

Domain ID domain_id	1u9mF00
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	47.044 Å
Unit-cell length b length_b	87.484 Å
Unit-cell length c length_c	138.383 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	35.550 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2660

fit	/app/data/saxs_computation/u9/1u9m/1u9m.fit
pddf	/app/data/pr_computation/u9/1u9m/1u9m.pr.out
profile	/app/data/saxs_computation/u9/1u9m/1u9m.dat

Crystal structure of F58W mutant of cytochrome b5

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

Refinement Refinement

Diffraction experiment Diffraction