SAXSdb — 4bry

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

GEMININ

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 83–160	Fragment：COILED-COIL, RESIDUES 83-160	MULTICILIN × 1 （D6RGH6） 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

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 4BRY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1T6F Crystal Structure of the Coiled-coil Dimerization Motif of Geminin Deposited 2004-05-06	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 109–145（37 aa） Fragment：COILED-COIL DOMAIN Chain B 109–145（37 aa） Fragment：COILED-COIL DOMAIN	Mutation：A1T Mutation：A1T	No recorded non-water small molecule	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
1UII Crystal structure of Geminin coiled-coil domain Deposited 2003-07-16	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 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 ligand/ion 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 ligand/ion 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
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01	Different construct 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 ligand/ion 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 1–78； UniProt 83–160

MULTICILIN

HOMO SAPIENS

UniProt D6RGH6

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 173–245	Fragment：COILED-COIL, RESIDUES 173-245	GEMININ × 1 （O75496） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	MCIN_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–73； UniProt 173–245

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	4bry
Deposition date deposition_date	2013-06-06
Structure title title	The Idas:Geminin heterodimeric parallel coiled-coil
Keywords keywords	CELL CYCLE, DNA REPLICATION LICENSING; 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	28.28 Å
Radius of gyration Rg (electron density) rg_electron	29.61 Å
Forward intensity I(0) i0	5407570.00
Molecular weight molecular_weight	16761.0 kDa
Excluded volume excluded_volume	20788 Å³
Envelope volume envelope_volume	30423 Å³
Hydration-shell volume shell_volume	11158 Å³
Envelope diameter envelope_diameter	106.7 Å
Shell Rg shell_rg	28.74 Å
Envelope Rg envelope_rg	30.85 Å
Shape Rg shape_rg	29.63 Å
Total Rg total_rg	29.43 Å
Total atoms total_atoms	1175
Residues n_residues	138
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	110.6 Å
Rg (real space) rg_real	29.30 Å
Rg uncertainty (real space) rg_real_error	1.41 Å
I(0) (real space) i0_real	5.4080e+06
I(0) uncertainty (real space) i0_real_error	1.0160e+05
Rg (reciprocal space) rg_reciprocal	28.99 Å
I(0) (reciprocal space) i0_reciprocal	5406000.0000
Solution quality estimate total_estimate	0.5717
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	15.8 Å
Skewness Skewness skewness	0.692
Kurtosis Kurtosis kurtosis	-0.314
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	213000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.140; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.007; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	GEMININ
Molecular weight formula_weight	9376.6 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	1175

QESFDLMIKENPSSQYWKEVAEKRRKALYEALKENEKLHKEIEQKDNEIARLKKENKELAEVAEHVQYMAELIERLNG

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 polymer

Description description	MULTICILIN
Molecular weight formula_weight	8385.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PDVPPPEQYWKEVADQNQRALGDALVENNQLHVTLTQKQEEIASLKERNVQLKELASRTRHLASVLDKLMITQ

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 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4brya_
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	d4bryb_
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.1.28.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4bryA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1180 — Geminin coiled-coil domain

Domain ID domain_id	4bryB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1180 — Geminin coiled-coil domain

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8. Citations (1)

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Unit-cell length a length_a	117.799 Å
Unit-cell length b length_b	117.799 Å
Unit-cell length c length_c	103.462 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	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	46.946 Å
R factor r_factor	0.2040
R_work r_work	0.2026
R_free r_free	0.2260

fit	/app/data/saxs_computation/br/4bry/4bry.fit
pddf	/app/data/pr_computation/br/4bry/4bry.pr.out
profile	/app/data/saxs_computation/br/4bry/4bry.dat

The Idas:Geminin heterodimeric parallel coiled-coil

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

MULTICILIN

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)