SAXSdb — 6g8t

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–118	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

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 6G8T	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 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
6G8W 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 homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 108–204（97 aa） Chain B 108–204（97 aa）	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

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 1–118； UniProt 1–118

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	6g8t
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	;PDZ1 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	15.20 Å
Radius of gyration Rg (electron density) rg_electron	13.89 Å
Forward intensity I(0) i0	3001250.00
Molecular weight molecular_weight	11999.0 kDa
Excluded volume excluded_volume	15018 Å³
Envelope volume envelope_volume	17677 Å³
Hydration-shell volume shell_volume	11144 Å³
Envelope diameter envelope_diameter	51.7 Å
Shell Rg shell_rg	19.32 Å
Envelope Rg envelope_rg	14.35 Å
Shape Rg shape_rg	13.86 Å
Total Rg total_rg	15.19 Å
Total atoms total_atoms	845
Residues n_residues	106
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	50.5 Å
Rg (real space) rg_real	15.14 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	3.0010e+06
I(0) uncertainty (real space) i0_real_error	3.4110e+04
Rg (reciprocal space) rg_reciprocal	15.14 Å
I(0) (reciprocal space) i0_reciprocal	3001000.0000
Solution quality estimate total_estimate	0.6484
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.8 Å
Skewness Skewness skewness	0.238
Kurtosis Kurtosis kurtosis	-0.198
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	429700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 0.998; Sysdev: 0.368; Positv: 1.000; Valcen: 0.997; 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	Golgi reassembly-stacking protein 1
Molecular weight formula_weight	13020.9 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	864

MGLGVSAEQPAGGAEGFHLHGVQENSPAQQAGLEPYFDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVFNMKTMRVREVEVVPSNMWGGQGLLGASVRFCSFRRASEQVWHVLDV

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	GLYCEROL
Molecular weight formula_weight	92.1 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	11

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6g8tA00
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	46.377 Å
Unit-cell length b length_b	63.163 Å
Unit-cell length c length_c	80.805 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.670 Å
Low-resolution limit resolution_low	33.930 Å
R factor r_factor	0.2114
R_work r_work	0.2088
R_free r_free	0.2579

fit	/app/data/saxs_computation/g8/6g8t/6g8t.fit
pddf	/app/data/pr_computation/g8/6g8t/6g8t.pr.out
profile	/app/data/saxs_computation/g8/6g8t/6g8t.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