SAXSdb — 1vkk

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

Glia maturation factor gamma

Mus musculus

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 1–142	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION,SITTING DROP,NANODROP；pH 8.5；277 K；30% PEG-4000, 0.1M Tris hydrochloride pH 8.5,0.2M lithium sulfate monohydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K	Resolution 1.35 Å R-free 0.194

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 1VKK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WFS Solution Structure of Glia Maturation Factor-gamma from Mus Musculus Deposited 2004-05-26	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–139（138 aa） Fragment：COFILIN-ADF-domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.21mM cofilin U-15N,13C; 20mM phosphate buffer Na; 100mM NaCl; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
4JD2 Crystal structure of Bos taurus Arp2/3 complex binding with Mus musculus GMF Deposited 2013-02-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain H 1–142（142 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.08 Å R-free 0.248

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

View Construct and Data Evidence

UniProt name	GMFG_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–154； UniProt 1–142

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	1vkk
Deposition date deposition_date	2004-05-27
Structure title title	Crystal structure of Glia maturation factor-gamma (GMFG) from Mus musculus at 1.50 A resolution
Keywords keywords	;15079298, GMFG, GLIA MATURATION FACTOR-GAMMA, STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, HORMONE-GROWTH FACTOR COMPLEX ;; HORMONE/GROWTH FACTOR
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	16.24 Å
Radius of gyration Rg (electron density) rg_electron	14.74 Å
Forward intensity I(0) i0	5025640.00
Molecular weight molecular_weight	16218.0 kDa
Excluded volume excluded_volume	20377 Å³
Envelope volume envelope_volume	22781 Å³
Hydration-shell volume shell_volume	13164 Å³
Envelope diameter envelope_diameter	53.5 Å
Shell Rg shell_rg	20.62 Å
Envelope Rg envelope_rg	15.16 Å
Shape Rg shape_rg	14.71 Å
Total Rg total_rg	15.96 Å
Total atoms total_atoms	1138
Residues n_residues	137
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	53.8 Å
Rg (real space) rg_real	16.17 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	5.0260e+06
I(0) uncertainty (real space) i0_real_error	5.9290e+04
Rg (reciprocal space) rg_reciprocal	16.17 Å
I(0) (reciprocal space) i0_reciprocal	5026000.0000
Solution quality estimate total_estimate	0.6450
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.242
Kurtosis Kurtosis kurtosis	-0.198
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1161000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 0.353; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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	Glia maturation factor gamma
Molecular weight formula_weight	18233.0 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	1342

MGSDKIHHHHHHMSDSLVVCEVDPELKETLRKFRFRKETNNAAIIMKVDKDRQMVVLEDELQNISPEELKLELPERQPRFVVYSYKYVHDDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAELTKVFEIRTTDDLTETWLKEKLAFFR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 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	183

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1vkka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.2 — Cofilin-like

CATH v4.4 (1 domains)

Domain ID domain_id	1vkkA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

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8. Citations (1)

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Unit-cell length a length_a	29.049 Å
Unit-cell length b length_b	34.605 Å
Unit-cell length c length_c	38.365 Å
Unit-cell angle α angle_alpha	69.95 °
Unit-cell angle β angle_beta	87.51 °
Unit-cell angle γ angle_gamma	70.46 °
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	—

Resolution resolution	1.350 Å
Low-resolution limit resolution_low	35.920 Å
R factor r_factor	0.1600
R_work r_work	0.1581
R_free r_free	0.1941

fit	/app/data/saxs_computation/vk/1vkk/1vkk.fit
pddf	/app/data/pr_computation/vk/1vkk/1vkk.pr.out
profile	/app/data/saxs_computation/vk/1vkk/1vkk.dat

Crystal structure of Glia maturation factor-gamma (GMFG) from Mus musculus at 1.50 A resolution

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

Glia maturation factor gamma

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