SAXSdb — 1mqv

▼

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

;CYTOCHROME C' ;

Rhodopseudomonas palustris

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 1–125	Mutation：Q1A, F32W, W72F	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.78 Å R-free 0.265
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–125	Mutation：Q1A, F32W, W72F	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.78 Å R-free 0.265

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 1MQV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A7V CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS Deposited 1998-03-18	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 1–125（125 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.30 Å R-free 0.241
1A7V CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS Deposited 1998-03-18	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 1–125（125 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.30 Å R-free 0.241

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYCP_RHOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 1–125 Author chain B； PDBConstruct 1–125； UniProt 1–125

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1mqv
Deposition date deposition_date	2002-09-17
Structure title title	Crystal Structure of the Q1A/F32W/W72F mutant of Rhodopseudomonas palustris cytochrome c' (prime) expressed in E. coli
Keywords keywords	Four-Helix Bundle, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	20.99 Å
Radius of gyration Rg (electron density) rg_electron	20.23 Å
Forward intensity I(0) i0	12474800.00
Molecular weight molecular_weight	26927.0 kDa
Excluded volume excluded_volume	34043 Å³
Envelope volume envelope_volume	39786 Å³
Hydration-shell volume shell_volume	17364 Å³
Envelope diameter envelope_diameter	72.7 Å
Shell Rg shell_rg	25.63 Å
Envelope Rg envelope_rg	20.54 Å
Shape Rg shape_rg	20.21 Å
Total Rg total_rg	21.15 Å
Total atoms total_atoms	1888
Residues n_residues	246
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

▼

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

Maximum dimension Dmax dmax	73.0 Å
Rg (real space) rg_real	21.05 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	1.2470e+07
I(0) uncertainty (real space) i0_real_error	1.6620e+05
Rg (reciprocal space) rg_reciprocal	21.04 Å
I(0) (reciprocal space) i0_reciprocal	12470000.0000
Solution quality estimate total_estimate	0.7879
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.429
Kurtosis Kurtosis kurtosis	-0.191
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3378000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;CYTOCHROME C' ;
Molecular weight formula_weight	13095.1 kDa
Mutation mutation	Q1A, F32W, W72F
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2153

ATDVIAQRKAILKQMGEATKPIAAMLKGEAKWDQAVVQKSLAAIADDSKKLPALFPADSKTGGDTAALPKIFEDKAKFDDLFAKLAAAATAAQGTIKDEASLKANIGGVLGNCKSCHDDFRAKKS

来源 Source

来源生物 organism	Rhodopseudomonas palustris
NCBI Class编号 ncbi_taxonomy_id	1076
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	265

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1mqva_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d1mqvb_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

CATH v4.4 (2 domains)

Domain ID domain_id	1mqvA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	10 — Cytochrome c/b562

Domain ID domain_id	1mqvB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	10 — Cytochrome c/b562

▶

8. Citations (1)

▶

Unit-cell length a length_a	33.839 Å
Unit-cell length b length_b	62.085 Å
Unit-cell length c length_c	113.419 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	8

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

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	42.000 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2650

fit	/app/data/saxs_computation/mq/1mqv/1mqv.fit
pddf	/app/data/pr_computation/mq/1mqv/1mqv.pr.out
profile	/app/data/saxs_computation/mq/1mqv/1mqv.dat

Crystal Structure of the Q1A/F32W/W72F mutant of Rhodopseudomonas palustris cytochrome c' (prime) expressed in E. coli

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

;CYTOCHROME C' ;

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