SAXSdb — 1t6f

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

Geminin

OrganismNot specified

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 109–145 Chain B； UniProt 109–145	Fragment：COILED-COIL DOMAIN Mutation：A1T	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；10% PEG 6000, 5% MPD, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.47 Å R-free 0.221

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 1T6F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1UII Crystal structure of Geminin coiled-coil domain Deposited 2003-07-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 70–152（83 aa） Fragment：coiled-coil domain Chain B 70–152（83 aa） Fragment：coiled-coil domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；0.36M Sodium Acetate, 0.1M TRIS, 30% PEG 4000, pH 8.5, EVAPORATION, temperature 293K	Resolution 2.00 Å R-free 0.239
2LP0 The solution structure of homeodomain-protein complex Deposited 2012-01-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 171–190（20 aa） Fragment：UNP residues 171-190	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；296 K；Ionic strength (raw mmCIF value) 0.125；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] Hox-C9-1, 1.0 mM Geminin-2, 25 mM potassium phosphate-3, 100 mM sodium chloride-4, 5 mM DTT-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM Hox-C9-6, 0.8 mM [U-100% 13C; U-100% 15N] Geminin-7, 25 mM potassium phosphate-8, 100 mM sodium chloride-9, 5 mM DTT-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] Hox-C9-11, 1.0 mM Geminin-12, 25 mM potassium phosphate-13, 100 mM sodium chloride-14, 5 mM DTT-15, 100% D2O \| 100% D2O NMR sample composition 1.0 mM Hox-C9-16, 0.8 mM [U-100% 13C; U-100% 15N] Geminin-17, 25 mM potassium phosphate-18, 100 mM sodium chloride-19, 5 mM DTT-20, 100% D2O \| 100% D2O	Resolution not provided
2WVR Human Cdt1:Geminin complex Deposited 2009-10-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PH 7.5 100-150 MM NACL CAPILLARY GRADIENT	Resolution 3.30 Å R-free 0.301
4BRY The Idas:Geminin heterodimeric parallel coiled-coil Deposited 2013-06-06	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 83–160（78 aa） Fragment：COILED-COIL, RESIDUES 83-160	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M SPG PH 7.5, 10 % ISOPROPANOL	Resolution 2.89 Å R-free 0.226
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01	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 C 195–209（15 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350	Resolution 3.40 Å R-free 0.241
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 195–209（15 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350	Resolution 3.40 Å R-free 0.241

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GEMI_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–37； UniProt 109–145 Author chain B； PDBConstruct 1–37； UniProt 109–145

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	1t6f
Deposition date deposition_date	2004-05-06
Structure title title	Crystal Structure of the Coiled-coil Dimerization Motif of Geminin
Keywords keywords	COILED-COIL, CELL CYCLE; CELL CYCLE
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	16.58 Å
Radius of gyration Rg (electron density) rg_electron	16.78 Å
Forward intensity I(0) i0	1640860.00
Molecular weight molecular_weight	8788.0 kDa
Excluded volume excluded_volume	11032 Å³
Envelope volume envelope_volume	13582 Å³
Hydration-shell volume shell_volume	8176 Å³
Envelope diameter envelope_diameter	61.2 Å
Shell Rg shell_rg	19.86 Å
Envelope Rg envelope_rg	17.25 Å
Shape Rg shape_rg	16.76 Å
Total Rg total_rg	17.49 Å
Total atoms total_atoms	618
Residues n_residues	74
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	60.5 Å
Rg (real space) rg_real	16.91 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	1.6410e+06
I(0) uncertainty (real space) i0_real_error	2.0830e+04
Rg (reciprocal space) rg_reciprocal	16.88 Å
I(0) (reciprocal space) i0_reciprocal	1641000.0000
Solution quality estimate total_estimate	0.6831
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	14.1 Å
Skewness Skewness skewness	0.663
Kurtosis Kurtosis kurtosis	-0.114
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	263000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.528; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.294; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1t6fa_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.28 — Geminin coiled-coil domain
Family Family family	h.1.28.1 — Geminin coiled-coil domain

Domain ID domain_id	d1t6fb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.28 — Geminin coiled-coil domain
Family Family family	h.1.28.1 — Geminin coiled-coil domain

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8. Citations (1)

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Unit-cell length a length_a	25.120 Å
Unit-cell length b length_b	43.440 Å
Unit-cell length c length_c	67.500 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	1.470 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1806
R_work r_work	0.1787
R_free r_free	0.2210

Description description	Geminin
Molecular weight formula_weight	4405.0 kDa
Mutation mutation	A1T
Source method src_method	syn
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	751

Crystal Structure of the Coiled-coil Dimerization Motif of Geminin

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

Geminin

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

fit	/app/data/saxs_computation/t6/1t6f/1t6f.fit
pddf	/app/data/pr_computation/t6/1t6f/1t6f.pr.out
profile	/app/data/saxs_computation/t6/1t6f/1t6f.dat