SAXSdb — 7cy1

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

Mutual gliding motility protein C

Myxococcus xanthus DK 1622

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 1–120	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；2.8 M Sodium Acetate Trihydrate pH 7.0	Resolution 2.19 Å R-free 0.227

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 7CY1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7CT3 Crystal Structure of MglC from Myxococcus xanthus Deposited 2020-08-17	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；0.2 M Lithium Sulfate Monohydrate, 0.1 M Tris-HCl pH 8.5, 30% w/v PEG 4000	Resolution 1.85 Å R-free 0.215

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

View Construct and Data Evidence

UniProt name	Q1D0B6_MYXXD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–120； UniProt 1–120

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	7cy1
Deposition date deposition_date	2020-09-03
Structure title title	Crystal Structure of MglC from Myxococcus xanthus
Keywords keywords	Roadblock/LC7 domain, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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	14.81 Å
Radius of gyration Rg (electron density) rg_electron	13.35 Å
Forward intensity I(0) i0	3446510.00
Molecular weight molecular_weight	13124.0 kDa
Excluded volume excluded_volume	16483 Å³
Envelope volume envelope_volume	18247 Å³
Hydration-shell volume shell_volume	11617 Å³
Envelope diameter envelope_diameter	44.1 Å
Shell Rg shell_rg	19.12 Å
Envelope Rg envelope_rg	13.65 Å
Shape Rg shape_rg	13.35 Å
Total Rg total_rg	14.61 Å
Total atoms total_atoms	922
Residues n_residues	120
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	46.6 Å
Rg (real space) rg_real	14.70 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	3.4470e+06
I(0) uncertainty (real space) i0_real_error	3.8420e+04
Rg (reciprocal space) rg_reciprocal	14.71 Å
I(0) (reciprocal space) i0_reciprocal	3447000.0000
Solution quality estimate total_estimate	0.8866
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.1 Å
Skewness Skewness skewness	0.114
Kurtosis Kurtosis kurtosis	-0.367
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1084000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.991

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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	Mutual gliding motility protein C
Molecular weight formula_weight	13134.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	962

MSFRTHLESVVNQVEGALACSVMGFDGISVDTFQKDESAELDLNGAWVEYANLLTQLRNAAETLKTGTVSEVSVNSEKVLTVMRLVSPDYFLVLALHADGNFGKGRYVLRVTAPKVRAEL

来源 Source

来源生物 organism	Myxococcus xanthus DK 1622
NCBI Class编号 ncbi_taxonomy_id	246197
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7cy1A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

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8. Citations (1)

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Unit-cell length a length_a	96.910 Å
Unit-cell length b length_b	96.910 Å
Unit-cell length c length_c	58.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.190 Å
Low-resolution limit resolution_low	27.980 Å
R factor r_factor	0.1904
R_work r_work	0.1882
R_free r_free	0.2269

fit	/app/data/saxs_computation/cy/7cy1/7cy1.fit
pddf	/app/data/pr_computation/cy/7cy1/7cy1.pr.out
profile	/app/data/saxs_computation/cy/7cy1/7cy1.dat

Crystal Structure of MglC from Myxococcus xanthus

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

Mutual gliding motility protein 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