SAXSdb — 6g8w

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

Golgi reassembly-stacking protein 1

Homo sapiens

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 108–204 Chain B； UniProt 108–204	Not recorded	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；1.4M Na/K phosphate pH 8.2	Resolution 2.12 Å R-free 0.235

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 6G8W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4REY Crystal Structure of the GRASP65-GM130 C-terminal peptide complex Deposited 2014-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–210（209 aa） Fragment：GRASP domain of GRAS65, UNP residues 1-210	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；291 K；30% PEG 4000, 0.1M Tris, 0.2M Lithium sulfate, , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.96 Å R-free 0.190
6G8T Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130 Deposited 2018-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–118（118 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；24% PEG1500, 20% glycerol	Resolution 2.67 Å R-free 0.258

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

View Construct and Data Evidence

UniProt name	GORS1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 108–204 Author chain B； PDBConstruct 1–97； UniProt 108–204

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	6g8w
Deposition date deposition_date	2018-04-10
Structure title title	Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130
Keywords keywords	;PDZ2 domain structure, Golgi stacking, GRASP family, Golgins, Golgi apparatus, yeast homolog of GRASP65, vesicle transport, PROTEIN BINDING ;; PROTEIN BINDING
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	18.38 Å
Radius of gyration Rg (electron density) rg_electron	17.54 Å
Forward intensity I(0) i0	7488080.00
Molecular weight molecular_weight	19794.0 kDa
Excluded volume excluded_volume	24661 Å³
Envelope volume envelope_volume	30583 Å³
Hydration-shell volume shell_volume	15061 Å³
Envelope diameter envelope_diameter	63.2 Å
Shell Rg shell_rg	22.91 Å
Envelope Rg envelope_rg	17.97 Å
Shape Rg shape_rg	17.54 Å
Total Rg total_rg	18.46 Å
Total atoms total_atoms	1394
Residues n_residues	179
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	63.9 Å
Rg (real space) rg_real	18.38 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	7.4880e+06
I(0) uncertainty (real space) i0_real_error	9.0460e+04
Rg (reciprocal space) rg_reciprocal	18.38 Å
I(0) (reciprocal space) i0_reciprocal	7488000.0000
Solution quality estimate total_estimate	0.7047
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.390
Kurtosis Kurtosis kurtosis	-0.080
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1180000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 0.330; Positv: 1.000; Valcen: 0.989; Smooth: 0.965

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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	Golgi reassembly-stacking protein 1
Molecular weight formula_weight	10552.7 kDa
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	1494

ASEQVWHVLDVEPSSPAALAGLRPYTDYVVGSDQILQESEDFFTLIESHEGKPLKLMVYNSKSDSCREVTVTPNAAWGGEGSLGCGIGYGYLHRIPT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	94

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6g8wA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	6g8wB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (1)

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Unit-cell length a length_a	50.825 Å
Unit-cell length b length_b	82.613 Å
Unit-cell length c length_c	49.220 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.120 Å
Low-resolution limit resolution_low	26.850 Å
R factor r_factor	0.1884
R_work r_work	0.1860
R_free r_free	0.2355

fit	/app/data/saxs_computation/g8/6g8w/6g8w.fit
pddf	/app/data/pr_computation/g8/6g8w/6g8w.pr.out
profile	/app/data/saxs_computation/g8/6g8w/6g8w.dat

Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130

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

Golgi reassembly-stacking protein 1

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